Starting phenix.real_space_refine on Thu Jul 2 06:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgf_44511/07_2026/9bgf_44511.cif" } resolution = 2.9 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= 0.001 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 Mg 4 5.21 5 S 37 5.16 5 C 4638 2.51 5 N 1238 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7317 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3650 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "B" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3471 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 396} Chain breaks: 3 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 2, 'NAG': 4, 'UD1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 69 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 2, 'NAG': 2, 'UD1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 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: 1.44, per 1000 atoms: 0.20 Number of scatterers: 7317 At special positions: 0 Unit cell: (72.864, 102.672, 111.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 37 16.00 P 4 15.00 Mg 4 11.99 O 1394 8.00 N 1238 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS B 70 " distance=2.03 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 C 1 " - " NAG C 2 " NAG-ASN " NAG A1304 " - " ASN A1129 " " NAG A1305 " - " ASN A 376 " " NAG A1306 " - " ASN A 83 " " NAG A1307 " - " ASN A1009 " " NAG B1301 " - " ASN B1129 " " NAG B1304 " - " ASN B 376 " " NAG C 1 " - " ASN B 83 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 283.0 milliseconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 51.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 removed outlier: 4.233A pdb=" N TYR A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.547A pdb=" N GLU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.584A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 376 through 380 removed outlier: 4.266A pdb=" N HIS A 379 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 931 through 947 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 983 Processing helix chain 'A' and resid 992 through 1002 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1043 through 1061 Processing helix chain 'A' and resid 1088 through 1093 Processing helix chain 'A' and resid 1094 through 1105 Processing helix chain 'A' and resid 1129 through 1143 removed outlier: 3.606A pdb=" N GLY A1135 " --> pdb=" O SER A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1176 removed outlier: 4.582A pdb=" N THR A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1203 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 85 through 98 removed outlier: 4.015A pdb=" N LEU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 3.597A pdb=" N TYR B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.616A pdb=" N HIS B 379 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'B' and resid 384 through 391 removed outlier: 3.919A pdb=" N HIS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 removed outlier: 4.143A pdb=" N ILE B 395 " --> pdb=" O ILE B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 931 through 947 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 983 Processing helix chain 'B' and resid 992 through 1002 Processing helix chain 'B' and resid 1009 through 1018 Processing helix chain 'B' and resid 1026 through 1038 Processing helix chain 'B' and resid 1043 through 1060 Processing helix chain 'B' and resid 1088 through 1093 Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1159 through 1176 removed outlier: 4.197A pdb=" N THR B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.467A pdb=" N ILE A 346 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A 368 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE A 348 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 76 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 405 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 78 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 6.342A pdb=" N ALA A1122 " --> pdb=" O CYS A1149 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN A1151 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS A1124 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.703A pdb=" N VAL A 953 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.502A pdb=" N GLN A 427 " --> pdb=" O GLU A1114 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET A1116 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 429 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1006 removed outlier: 4.524A pdb=" N LYS A1108 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1024 through 1025 removed outlier: 4.596A pdb=" N VAL A1086 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 369 removed outlier: 6.626A pdb=" N ILE B 346 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 368 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 348 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 76 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 405 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 78 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 4.814A pdb=" N TRP B 433 " --> pdb=" O VAL B 953 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.589A pdb=" N GLN B 427 " --> pdb=" O GLU B1114 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N MET B1116 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 429 " --> pdb=" O MET B1116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1005 through 1006 removed outlier: 4.556A pdb=" N LYS B1108 " --> pdb=" O GLN B1006 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1024 through 1025 removed outlier: 4.566A pdb=" N VAL B1086 " --> pdb=" O LEU B1025 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 852 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: 0.73 Time building geometry restraints manager: 0.54 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: 1558 1.33 - 1.45: 1762 1.45 - 1.57: 4099 1.57 - 1.69: 8 1.69 - 1.81: 66 Bond restraints: 7493 Sorted by residual: bond pdb=" N THR B1128 " pdb=" CA THR B1128 " ideal model delta sigma weight residual 1.460 1.475 -0.015 1.54e-02 4.22e+03 9.87e-01 bond pdb=" CA TRP A 416 " pdb=" C TRP A 416 " ideal model delta sigma weight residual 1.519 1.529 -0.009 9.50e-03 1.11e+04 9.86e-01 bond pdb=" C TRP A 416 " pdb=" O TRP A 416 " ideal model delta sigma weight residual 1.236 1.227 0.009 8.90e-03 1.26e+04 9.21e-01 bond pdb=" C1 NAG A1305 " pdb=" C2 NAG A1305 " ideal model delta sigma weight residual 1.532 1.549 -0.017 2.00e-02 2.50e+03 7.07e-01 bond pdb=" CA PHE A 982 " pdb=" CB PHE A 982 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.78e-02 3.16e+03 5.99e-01 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 9988 1.61 - 3.23: 134 3.23 - 4.84: 23 4.84 - 6.46: 4 6.46 - 8.07: 1 Bond angle restraints: 10150 Sorted by residual: angle pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " pdb=" C5 NAG A1305 " ideal model delta sigma weight residual 113.21 121.28 -8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" C ARG A1127 " pdb=" N THR A1128 " pdb=" CA THR A1128 " ideal model delta sigma weight residual 121.54 126.23 -4.69 1.91e+00 2.74e-01 6.02e+00 angle pdb=" C SER B 319 " pdb=" N ALA B 320 " pdb=" CA ALA B 320 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C PHE B 998 " pdb=" N TYR B 999 " pdb=" CA TYR B 999 " ideal model delta sigma weight residual 122.38 118.18 4.20 1.81e+00 3.05e-01 5.38e+00 angle pdb=" N THR A1128 " pdb=" CA THR A1128 " pdb=" C THR A1128 " ideal model delta sigma weight residual 110.80 115.33 -4.53 2.13e+00 2.20e-01 4.52e+00 ... (remaining 10145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.94: 4342 18.94 - 37.89: 258 37.89 - 56.83: 70 56.83 - 75.78: 18 75.78 - 94.72: 12 Dihedral angle restraints: 4700 sinusoidal: 2148 harmonic: 2552 Sorted by residual: dihedral pdb=" CA VAL A 349 " pdb=" C VAL A 349 " pdb=" N THR A 350 " pdb=" CA THR A 350 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A 999 " pdb=" C TYR A 999 " pdb=" N TYR A1000 " pdb=" CA TYR A1000 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TYR B 999 " pdb=" C TYR B 999 " pdb=" N TYR B1000 " pdb=" CA TYR B1000 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 631 0.027 - 0.054: 301 0.054 - 0.082: 96 0.082 - 0.109: 62 0.109 - 0.136: 29 Chirality restraints: 1119 Sorted by residual: 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 -2.39 -0.01 2.00e-02 2.50e+03 5.04e-01 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA THR A1128 " pdb=" N THR A1128 " pdb=" C THR A1128 " pdb=" CB THR A1128 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1116 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 72 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 982 " 0.008 2.00e-02 2.50e+03 1.02e-02 1.83e+00 pdb=" CG PHE A 982 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 982 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 982 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 982 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 982 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 982 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 407 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C ASP B 407 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP B 407 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 408 " -0.007 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 61 2.50 - 3.10: 5263 3.10 - 3.70: 11426 3.70 - 4.30: 17066 4.30 - 4.90: 28085 Nonbonded interactions: 61901 Sorted by model distance: nonbonded pdb=" OD1 ASN B1151 " pdb="MG MG B1302 " model vdw 1.906 2.170 nonbonded pdb=" OD2 ASP B 408 " pdb="MG MG B1302 " model vdw 1.946 2.170 nonbonded pdb="MG MG B1302 " pdb=" O2B UD1 B1303 " model vdw 1.951 2.170 nonbonded pdb=" OD1 ASN A1151 " pdb="MG MG A1308 " model vdw 1.981 2.170 nonbonded pdb=" O2B UD1 A1303 " pdb="MG MG A1308 " model vdw 2.026 2.170 ... (remaining 61896 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 'A' and (resid 49 through 105 or resid 316 through 1185 or resid 1306 or \ resid 1308)) selection = (chain 'B' and (resid 49 through 1185 or resid 1304 or resid 1306)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.080 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.003 0.024 7502 Z= 0.134 Angle : 0.529 8.074 10176 Z= 0.268 Chirality : 0.043 0.136 1119 Planarity : 0.004 0.045 1293 Dihedral : 14.494 94.720 3027 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.17 (0.30), residues: 841 helix: 1.59 (0.28), residues: 367 sheet: 0.74 (0.61), residues: 82 loop : 0.09 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 986 TYR 0.012 0.002 TYR B 937 PHE 0.023 0.002 PHE A 982 TRP 0.007 0.001 TRP B 81 HIS 0.003 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7493) covalent geometry : angle 0.52017 / 0.27 (10150) SS BOND : bond 0.00226 / 0.12 ( 1) SS BOND : angle 0.22266 / 0.12 ( 2) hydrogen bonds : bond 0.17776 / 12.33 ( 294) hydrogen bonds : angle 6.28958 / 4.43 ( 852) link_BETA1-4 : bond 0.00209 / 0.11 ( 1) link_BETA1-4 : angle 1.03110 / 0.58 ( 3) link_NAG-ASN : bond 0.00252 / 0.13 ( 7) link_NAG-ASN : angle 2.12017 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.241 Fit side-chains REVERT: A 94 GLN cc_start: 0.8028 (mt0) cc_final: 0.7786 (mt0) REVERT: A 1043 SER cc_start: 0.8020 (m) cc_final: 0.7738 (p) REVERT: A 1045 GLN cc_start: 0.7030 (mp10) cc_final: 0.6770 (mp10) REVERT: A 1170 ASP cc_start: 0.7787 (t70) cc_final: 0.7489 (t0) REVERT: A 1191 ARG cc_start: 0.6769 (mtm-85) cc_final: 0.4475 (mmt180) REVERT: B 55 SER cc_start: 0.8012 (t) cc_final: 0.7720 (p) REVERT: B 396 GLU cc_start: 0.8206 (tp30) cc_final: 0.7987 (tp30) REVERT: B 1002 MET cc_start: 0.8596 (mtp) cc_final: 0.8383 (mtm) REVERT: B 1016 GLU cc_start: 0.7484 (pt0) cc_final: 0.6964 (mt-10) outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.5912 time to fit residues: 73.2854 Evaluate side-chains 99 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0050 chunk 74 optimal weight: 0.9980 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN B1158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123833 restraints weight = 7447.124| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.28 r_work: 0.3333 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7502 Z= 0.119 Angle : 0.539 7.766 10176 Z= 0.276 Chirality : 0.043 0.145 1119 Planarity : 0.004 0.041 1293 Dihedral : 10.874 98.607 1214 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.61 % Allowed : 10.29 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.98 (0.30), residues: 841 helix: 1.45 (0.27), residues: 375 sheet: 0.71 (0.61), residues: 82 loop : -0.08 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.014 0.001 TYR B 937 PHE 0.032 0.002 PHE A 982 TRP 0.007 0.001 TRP B 416 HIS 0.009 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7493) covalent geometry : angle 0.53217 / 0.27 (10150) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.32396 / 0.17 ( 2) hydrogen bonds : bond 0.04411 / 3.04 ( 294) hydrogen bonds : angle 4.71946 / 3.31 ( 852) link_BETA1-4 : bond 0.00650 / 0.34 ( 1) link_BETA1-4 : angle 1.09541 / 0.63 ( 3) link_NAG-ASN : bond 0.00260 / 0.13 ( 7) link_NAG-ASN : angle 1.96049 / 1.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.193 Fit side-chains REVERT: A 94 GLN cc_start: 0.7572 (mt0) cc_final: 0.7322 (mt0) REVERT: A 1043 SER cc_start: 0.7352 (m) cc_final: 0.6805 (p) REVERT: A 1045 GLN cc_start: 0.6962 (mp10) cc_final: 0.6682 (mp10) REVERT: A 1053 MET cc_start: 0.7524 (mtp) cc_final: 0.7280 (mtt) REVERT: A 1125 MET cc_start: 0.8044 (mmm) cc_final: 0.7654 (mmm) REVERT: A 1191 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.4276 (mmt180) REVERT: B 55 SER cc_start: 0.7987 (t) cc_final: 0.7535 (p) REVERT: B 100 MET cc_start: 0.4658 (pmm) cc_final: 0.4027 (ttp) REVERT: B 396 GLU cc_start: 0.8247 (tp30) cc_final: 0.8020 (tp30) REVERT: B 1016 GLU cc_start: 0.7558 (pt0) cc_final: 0.6911 (mt-10) REVERT: B 1045 GLN cc_start: 0.7290 (mp10) cc_final: 0.6981 (mp10) outliers start: 13 outliers final: 5 residues processed: 110 average time/residue: 0.5439 time to fit residues: 63.1189 Evaluate side-chains 94 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN B 326 ASN B 362 ASN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119874 restraints weight = 7448.604| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.29 r_work: 0.3284 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7502 Z= 0.154 Angle : 0.556 7.527 10176 Z= 0.285 Chirality : 0.044 0.145 1119 Planarity : 0.004 0.040 1293 Dihedral : 10.723 100.025 1214 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.48 % Allowed : 10.90 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.30), residues: 841 helix: 1.39 (0.27), residues: 374 sheet: 0.53 (0.60), residues: 82 loop : -0.23 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 986 TYR 0.013 0.002 TYR B 937 PHE 0.029 0.002 PHE A 982 TRP 0.010 0.001 TRP A 416 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7493) covalent geometry : angle 0.55056 / 0.28 (10150) SS BOND : bond 0.00094 / 0.05 ( 1) SS BOND : angle 0.28455 / 0.15 ( 2) hydrogen bonds : bond 0.04295 / 2.89 ( 294) hydrogen bonds : angle 4.52283 / 3.19 ( 852) link_BETA1-4 : bond 0.00383 / 0.20 ( 1) link_BETA1-4 : angle 1.05786 / 0.60 ( 3) link_NAG-ASN : bond 0.00209 / 0.10 ( 7) link_NAG-ASN : angle 1.81705 / 1.01 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.298 Fit side-chains REVERT: A 325 ASP cc_start: 0.7605 (t0) cc_final: 0.7394 (t0) REVERT: A 371 GLN cc_start: 0.7807 (mm110) cc_final: 0.7466 (mp-120) REVERT: A 1045 GLN cc_start: 0.6959 (mp10) cc_final: 0.6689 (mp10) REVERT: A 1053 MET cc_start: 0.7563 (mtp) cc_final: 0.7301 (mtt) REVERT: A 1191 ARG cc_start: 0.6706 (mtm-85) cc_final: 0.4193 (mmt180) REVERT: B 55 SER cc_start: 0.8044 (t) cc_final: 0.7594 (p) REVERT: B 90 LEU cc_start: 0.7010 (tt) cc_final: 0.6734 (mp) REVERT: B 100 MET cc_start: 0.4615 (pmm) cc_final: 0.3949 (ttp) REVERT: B 396 GLU cc_start: 0.8273 (tp30) cc_final: 0.8042 (tp30) REVERT: B 1016 GLU cc_start: 0.7600 (pt0) cc_final: 0.6946 (mt-10) REVERT: B 1045 GLN cc_start: 0.7197 (mp10) cc_final: 0.6854 (mp10) outliers start: 20 outliers final: 9 residues processed: 114 average time/residue: 0.4916 time to fit residues: 59.4655 Evaluate side-chains 107 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120337 restraints weight = 7563.153| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.30 r_work: 0.3282 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7502 Z= 0.139 Angle : 0.544 7.437 10176 Z= 0.277 Chirality : 0.043 0.139 1119 Planarity : 0.004 0.039 1293 Dihedral : 10.755 101.242 1214 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.97 % Allowed : 11.28 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.79 (0.30), residues: 841 helix: 1.40 (0.28), residues: 374 sheet: 0.46 (0.59), residues: 82 loop : -0.28 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 986 TYR 0.013 0.002 TYR B 331 PHE 0.029 0.002 PHE A 982 TRP 0.009 0.001 TRP A 416 HIS 0.005 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7493) covalent geometry : angle 0.53854 / 0.28 (10150) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.24916 / 0.13 ( 2) hydrogen bonds : bond 0.03988 / 2.68 ( 294) hydrogen bonds : angle 4.42063 / 3.11 ( 852) link_BETA1-4 : bond 0.00429 / 0.23 ( 1) link_BETA1-4 : angle 1.09421 / 0.62 ( 3) link_NAG-ASN : bond 0.00201 / 0.10 ( 7) link_NAG-ASN : angle 1.79814 / 0.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.213 Fit side-chains REVERT: A 325 ASP cc_start: 0.7616 (t0) cc_final: 0.7331 (t0) REVERT: A 337 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 1045 GLN cc_start: 0.6888 (mp10) cc_final: 0.6688 (mp10) REVERT: A 1053 MET cc_start: 0.7528 (mtp) cc_final: 0.7283 (mtt) REVERT: A 1060 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5642 (mmm) REVERT: A 1170 ASP cc_start: 0.7929 (t70) cc_final: 0.7565 (t0) REVERT: A 1191 ARG cc_start: 0.6751 (mtm-85) cc_final: 0.4242 (mmt180) REVERT: B 55 SER cc_start: 0.8045 (t) cc_final: 0.7585 (p) REVERT: B 90 LEU cc_start: 0.7015 (tt) cc_final: 0.6745 (mp) REVERT: B 100 MET cc_start: 0.4728 (pmm) cc_final: 0.3920 (ttp) REVERT: B 992 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: B 1016 GLU cc_start: 0.7598 (pt0) cc_final: 0.6950 (mt-10) REVERT: B 1045 GLN cc_start: 0.7256 (mp10) cc_final: 0.6908 (mp10) outliers start: 24 outliers final: 11 residues processed: 120 average time/residue: 0.5045 time to fit residues: 64.1075 Evaluate side-chains 111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120173 restraints weight = 7502.734| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.29 r_work: 0.3297 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7502 Z= 0.137 Angle : 0.542 7.415 10176 Z= 0.276 Chirality : 0.043 0.146 1119 Planarity : 0.004 0.038 1293 Dihedral : 10.778 101.366 1214 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.97 % Allowed : 12.02 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.79 (0.30), residues: 841 helix: 1.43 (0.28), residues: 376 sheet: 0.34 (0.59), residues: 84 loop : -0.28 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 986 TYR 0.013 0.001 TYR B 937 PHE 0.029 0.002 PHE A 982 TRP 0.009 0.001 TRP A 416 HIS 0.006 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7493) covalent geometry : angle 0.53612 / 0.27 (10150) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 0.22464 / 0.12 ( 2) hydrogen bonds : bond 0.03924 / 2.62 ( 294) hydrogen bonds : angle 4.37435 / 3.08 ( 852) link_BETA1-4 : bond 0.00347 / 0.18 ( 1) link_BETA1-4 : angle 1.06260 / 0.60 ( 3) link_NAG-ASN : bond 0.00195 / 0.09 ( 7) link_NAG-ASN : angle 1.78277 / 0.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.288 Fit side-chains REVERT: A 325 ASP cc_start: 0.7600 (t0) cc_final: 0.7301 (t0) REVERT: A 371 GLN cc_start: 0.7807 (mm110) cc_final: 0.7496 (mp-120) REVERT: A 1053 MET cc_start: 0.7530 (mtp) cc_final: 0.7284 (mtt) REVERT: A 1170 ASP cc_start: 0.7927 (t70) cc_final: 0.7555 (t0) REVERT: A 1191 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.4221 (mmt180) REVERT: B 55 SER cc_start: 0.8056 (t) cc_final: 0.7584 (p) REVERT: B 90 LEU cc_start: 0.7025 (tt) cc_final: 0.6759 (mp) REVERT: B 100 MET cc_start: 0.4728 (pmm) cc_final: 0.3417 (tmt) REVERT: B 992 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: B 1002 MET cc_start: 0.8638 (mtp) cc_final: 0.8422 (mtm) REVERT: B 1016 GLU cc_start: 0.7598 (pt0) cc_final: 0.6939 (mt-10) REVERT: B 1045 GLN cc_start: 0.7235 (mp10) cc_final: 0.6930 (mp10) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.5290 time to fit residues: 65.4524 Evaluate side-chains 109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.0370 chunk 16 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120502 restraints weight = 7531.321| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.28 r_work: 0.3298 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7502 Z= 0.135 Angle : 0.546 7.415 10176 Z= 0.278 Chirality : 0.043 0.148 1119 Planarity : 0.004 0.037 1293 Dihedral : 10.806 101.121 1214 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.73 % Allowed : 12.64 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.75 (0.30), residues: 841 helix: 1.43 (0.28), residues: 377 sheet: -0.10 (0.55), residues: 94 loop : -0.24 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 986 TYR 0.014 0.001 TYR B 331 PHE 0.028 0.002 PHE A 982 TRP 0.008 0.001 TRP A 416 HIS 0.006 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7493) covalent geometry : angle 0.54007 / 0.28 (10150) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.29548 / 0.17 ( 2) hydrogen bonds : bond 0.03861 / 2.58 ( 294) hydrogen bonds : angle 4.35118 / 3.07 ( 852) link_BETA1-4 : bond 0.00378 / 0.20 ( 1) link_BETA1-4 : angle 1.05473 / 0.59 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 7) link_NAG-ASN : angle 1.75833 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.281 Fit side-chains REVERT: A 325 ASP cc_start: 0.7619 (t0) cc_final: 0.7327 (t0) REVERT: A 371 GLN cc_start: 0.7784 (mm110) cc_final: 0.7493 (mp-120) REVERT: A 1053 MET cc_start: 0.7516 (mtp) cc_final: 0.7292 (mtt) REVERT: A 1060 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5743 (mmm) REVERT: A 1191 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.4238 (mmt180) REVERT: B 55 SER cc_start: 0.8064 (t) cc_final: 0.7592 (p) REVERT: B 90 LEU cc_start: 0.7133 (tt) cc_final: 0.6852 (mp) REVERT: B 100 MET cc_start: 0.4690 (pmm) cc_final: 0.3445 (tmt) REVERT: B 992 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 1016 GLU cc_start: 0.7571 (pt0) cc_final: 0.6925 (mt-10) REVERT: B 1045 GLN cc_start: 0.7214 (mp10) cc_final: 0.6925 (mp10) outliers start: 22 outliers final: 14 residues processed: 121 average time/residue: 0.5151 time to fit residues: 65.8701 Evaluate side-chains 115 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 427 GLN B1158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122384 restraints weight = 7476.996| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.30 r_work: 0.3316 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7502 Z= 0.111 Angle : 0.524 7.599 10176 Z= 0.266 Chirality : 0.042 0.137 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.748 99.170 1214 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.23 % Allowed : 14.62 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.92 (0.30), residues: 841 helix: 1.60 (0.28), residues: 376 sheet: 0.29 (0.59), residues: 84 loop : -0.25 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 986 TYR 0.013 0.001 TYR B 937 PHE 0.027 0.001 PHE A 982 TRP 0.006 0.001 TRP A 416 HIS 0.007 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7493) covalent geometry : angle 0.51855 / 0.27 (10150) SS BOND : bond 0.00121 / 0.06 ( 1) SS BOND : angle 0.38205 / 0.21 ( 2) hydrogen bonds : bond 0.03557 / 2.38 ( 294) hydrogen bonds : angle 4.27710 / 3.02 ( 852) link_BETA1-4 : bond 0.00420 / 0.22 ( 1) link_BETA1-4 : angle 1.05800 / 0.60 ( 3) link_NAG-ASN : bond 0.00224 / 0.11 ( 7) link_NAG-ASN : angle 1.69840 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.272 Fit side-chains REVERT: A 325 ASP cc_start: 0.7673 (t0) cc_final: 0.7389 (t0) REVERT: A 371 GLN cc_start: 0.7748 (mm110) cc_final: 0.7506 (mp-120) REVERT: A 407 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.6859 (p0) REVERT: A 1053 MET cc_start: 0.7498 (mtp) cc_final: 0.7251 (mtt) REVERT: A 1060 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5744 (mmm) REVERT: A 1061 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4080 (tp) REVERT: B 55 SER cc_start: 0.8050 (t) cc_final: 0.7562 (p) REVERT: B 90 LEU cc_start: 0.7137 (tt) cc_final: 0.6858 (mp) REVERT: B 100 MET cc_start: 0.4857 (pmm) cc_final: 0.3574 (tmt) REVERT: B 992 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 1002 MET cc_start: 0.8567 (mtp) cc_final: 0.8366 (mtm) REVERT: B 1016 GLU cc_start: 0.7566 (pt0) cc_final: 0.6870 (mt-10) REVERT: B 1045 GLN cc_start: 0.7247 (mp10) cc_final: 0.6970 (mp10) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.4915 time to fit residues: 59.4404 Evaluate side-chains 109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 427 GLN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120034 restraints weight = 7522.314| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.29 r_work: 0.3292 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7502 Z= 0.145 Angle : 0.560 7.492 10176 Z= 0.284 Chirality : 0.044 0.158 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.789 100.135 1214 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.73 % Allowed : 14.62 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.79 (0.30), residues: 841 helix: 1.51 (0.28), residues: 376 sheet: -0.09 (0.55), residues: 94 loop : -0.26 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 986 TYR 0.014 0.002 TYR B 331 PHE 0.028 0.002 PHE A 982 TRP 0.008 0.001 TRP A 416 HIS 0.008 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7493) covalent geometry : angle 0.55431 / 0.28 (10150) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 0.26776 / 0.15 ( 2) hydrogen bonds : bond 0.03863 / 2.58 ( 294) hydrogen bonds : angle 4.33410 / 3.06 ( 852) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 1.06972 / 0.60 ( 3) link_NAG-ASN : bond 0.00174 / 0.08 ( 7) link_NAG-ASN : angle 1.74377 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.227 Fit side-chains REVERT: A 325 ASP cc_start: 0.7716 (t0) cc_final: 0.7416 (t0) REVERT: A 371 GLN cc_start: 0.7778 (mm110) cc_final: 0.7504 (mp-120) REVERT: A 407 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 1053 MET cc_start: 0.7506 (mtp) cc_final: 0.7264 (mtt) REVERT: A 1060 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5788 (mmm) REVERT: A 1082 ASN cc_start: 0.8287 (p0) cc_final: 0.7984 (p0) REVERT: A 1170 ASP cc_start: 0.7914 (t70) cc_final: 0.7538 (t0) REVERT: B 55 SER cc_start: 0.8081 (t) cc_final: 0.7581 (p) REVERT: B 90 LEU cc_start: 0.7138 (tt) cc_final: 0.6859 (mp) REVERT: B 100 MET cc_start: 0.4901 (pmm) cc_final: 0.3600 (tmt) REVERT: B 992 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: B 1002 MET cc_start: 0.8614 (mtp) cc_final: 0.8398 (mtm) REVERT: B 1016 GLU cc_start: 0.7573 (pt0) cc_final: 0.6917 (mt-10) REVERT: B 1045 GLN cc_start: 0.7271 (mp10) cc_final: 0.6971 (mp-120) outliers start: 22 outliers final: 14 residues processed: 117 average time/residue: 0.4475 time to fit residues: 55.4853 Evaluate side-chains 112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119892 restraints weight = 7455.078| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.29 r_work: 0.3284 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7502 Z= 0.148 Angle : 0.572 7.359 10176 Z= 0.291 Chirality : 0.044 0.159 1119 Planarity : 0.004 0.035 1293 Dihedral : 10.838 100.363 1214 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.97 % Allowed : 14.50 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.72 (0.30), residues: 841 helix: 1.45 (0.28), residues: 376 sheet: -0.07 (0.55), residues: 94 loop : -0.31 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.013 0.002 TYR B 937 PHE 0.029 0.002 PHE A 982 TRP 0.009 0.001 TRP A 416 HIS 0.009 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7493) covalent geometry : angle 0.56664 / 0.29 (10150) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.23539 / 0.13 ( 2) hydrogen bonds : bond 0.03911 / 2.62 ( 294) hydrogen bonds : angle 4.35519 / 3.07 ( 852) link_BETA1-4 : bond 0.00369 / 0.19 ( 1) link_BETA1-4 : angle 1.06104 / 0.59 ( 3) link_NAG-ASN : bond 0.00160 / 0.08 ( 7) link_NAG-ASN : angle 1.72141 / 0.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.196 Fit side-chains REVERT: A 325 ASP cc_start: 0.7725 (t0) cc_final: 0.7456 (t0) REVERT: A 371 GLN cc_start: 0.7764 (mm110) cc_final: 0.7495 (mp-120) REVERT: A 1053 MET cc_start: 0.7504 (mtp) cc_final: 0.7280 (mtt) REVERT: A 1060 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5794 (mmm) REVERT: A 1082 ASN cc_start: 0.8300 (p0) cc_final: 0.7990 (p0) REVERT: A 1112 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7522 (ptm160) REVERT: B 55 SER cc_start: 0.8078 (t) cc_final: 0.7582 (p) REVERT: B 90 LEU cc_start: 0.7159 (tt) cc_final: 0.6869 (mp) REVERT: B 992 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 1002 MET cc_start: 0.8616 (mtp) cc_final: 0.8396 (mtm) REVERT: B 1016 GLU cc_start: 0.7551 (pt0) cc_final: 0.6884 (mt-10) REVERT: B 1045 GLN cc_start: 0.7250 (mp10) cc_final: 0.6950 (mp-120) outliers start: 24 outliers final: 13 residues processed: 119 average time/residue: 0.4580 time to fit residues: 57.6509 Evaluate side-chains 111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.0070 chunk 74 optimal weight: 0.0470 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 427 GLN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122151 restraints weight = 7442.314| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.29 r_work: 0.3317 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7502 Z= 0.115 Angle : 0.551 8.202 10176 Z= 0.280 Chirality : 0.042 0.154 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.795 99.179 1214 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.86 % Allowed : 16.11 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.87 (0.30), residues: 841 helix: 1.59 (0.28), residues: 376 sheet: 0.28 (0.59), residues: 84 loop : -0.32 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 375 TYR 0.013 0.001 TYR B 937 PHE 0.027 0.001 PHE A 982 TRP 0.006 0.001 TRP A 416 HIS 0.011 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7493) covalent geometry : angle 0.54577 / 0.28 (10150) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.39230 / 0.22 ( 2) hydrogen bonds : bond 0.03555 / 2.38 ( 294) hydrogen bonds : angle 4.28393 / 3.02 ( 852) link_BETA1-4 : bond 0.00469 / 0.25 ( 1) link_BETA1-4 : angle 1.05720 / 0.60 ( 3) link_NAG-ASN : bond 0.00213 / 0.10 ( 7) link_NAG-ASN : angle 1.65449 / 0.91 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.317 Fit side-chains REVERT: A 325 ASP cc_start: 0.7598 (t0) cc_final: 0.7329 (t0) REVERT: A 371 GLN cc_start: 0.7743 (mm110) cc_final: 0.7508 (mp-120) REVERT: A 407 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.6865 (p0) REVERT: A 1021 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8174 (mt0) REVERT: A 1053 MET cc_start: 0.7479 (mtp) cc_final: 0.7242 (mtt) REVERT: A 1060 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5789 (mmm) REVERT: B 55 SER cc_start: 0.8084 (t) cc_final: 0.7593 (p) REVERT: B 90 LEU cc_start: 0.7138 (tt) cc_final: 0.6840 (mp) REVERT: B 100 MET cc_start: 0.4577 (pmm) cc_final: 0.4189 (ttt) REVERT: B 992 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: B 1002 MET cc_start: 0.8593 (mtp) cc_final: 0.8374 (mtm) REVERT: B 1016 GLU cc_start: 0.7544 (pt0) cc_final: 0.6881 (mt-10) REVERT: B 1021 GLN cc_start: 0.8204 (mm110) cc_final: 0.7989 (mp-120) REVERT: B 1045 GLN cc_start: 0.7261 (mp10) cc_final: 0.6977 (mp-120) REVERT: B 1125 MET cc_start: 0.8001 (mtp) cc_final: 0.7730 (mtp) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.4932 time to fit residues: 57.2563 Evaluate side-chains 109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1012 GLN B 427 GLN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119545 restraints weight = 7470.980| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.30 r_work: 0.3285 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7502 Z= 0.155 Angle : 0.590 8.206 10176 Z= 0.301 Chirality : 0.044 0.168 1119 Planarity : 0.004 0.037 1293 Dihedral : 10.834 100.379 1214 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.73 % Allowed : 16.48 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.71 (0.30), residues: 841 helix: 1.47 (0.28), residues: 376 sheet: -0.09 (0.55), residues: 94 loop : -0.34 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 375 TYR 0.015 0.002 TYR B 331 PHE 0.028 0.002 PHE A 982 TRP 0.009 0.001 TRP A 416 HIS 0.011 0.001 HIS B 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 7493) covalent geometry : angle 0.58527 / 0.30 (10150) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.24432 / 0.14 ( 2) hydrogen bonds : bond 0.03924 / 2.63 ( 294) hydrogen bonds : angle 4.35064 / 3.07 ( 852) link_BETA1-4 : bond 0.00366 / 0.19 ( 1) link_BETA1-4 : angle 1.07375 / 0.60 ( 3) link_NAG-ASN : bond 0.00165 / 0.08 ( 7) link_NAG-ASN : angle 1.71265 / 0.93 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.65 seconds wall clock time: 63 minutes 12.65 seconds (3792.65 seconds total)