Starting phenix.real_space_refine on Sun May 11 02:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgf_44511/05_2025/9bgf_44511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgf_44511/05_2025/9bgf_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_44511/05_2025/9bgf_44511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgf_44511/05_2025/9bgf_44511.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgf_44511/05_2025/9bgf_44511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgf_44511/05_2025/9bgf_44511.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 98 Unusual residues: {' CA': 1, ' MG': 2, 'NAG': 4, 'UD1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 70 Unusual residues: {' CA': 1, ' MG': 2, 'NAG': 2, 'UD1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.10, per 1000 atoms: 0.70 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: 1.87 Conformation dependent library (CDL) restraints added in 922.9 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: 0.87 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: 2.39 Time building geometry restraints manager: 2.14 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: 3.530 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 20.740 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (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 TRP 0.007 0.001 TRP B 81 HIS 0.003 0.001 HIS B1158 PHE 0.023 0.002 PHE A 982 TYR 0.012 0.002 TYR B 937 ARG 0.003 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 7) link_NAG-ASN : angle 2.12017 ( 21) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.03110 ( 3) hydrogen bonds : bond 0.17776 ( 294) hydrogen bonds : angle 6.28958 ( 852) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.22266 ( 2) covalent geometry : bond 0.00302 ( 7493) covalent geometry : angle 0.52017 (10150) *********************** 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 : 0.830 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: 1.2148 time to fit residues: 151.3128 Evaluate side-chains 98 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN B 326 ASN B 362 ASN B 967 GLN ** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117864 restraints weight = 7490.969| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.24 r_work: 0.3256 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7502 Z= 0.218 Angle : 0.638 7.956 10176 Z= 0.328 Chirality : 0.047 0.166 1119 Planarity : 0.005 0.044 1293 Dihedral : 11.019 103.318 1214 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.48 % Allowed : 9.79 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 841 helix: 1.10 (0.27), residues: 374 sheet: 0.66 (0.60), residues: 82 loop : -0.28 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 416 HIS 0.009 0.001 HIS A 379 PHE 0.033 0.003 PHE A 982 TYR 0.015 0.002 TYR B 404 ARG 0.005 0.001 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 7) link_NAG-ASN : angle 2.00143 ( 21) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 1.07356 ( 3) hydrogen bonds : bond 0.05166 ( 294) hydrogen bonds : angle 4.83610 ( 852) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.37851 ( 2) covalent geometry : bond 0.00514 ( 7493) covalent geometry : angle 0.63216 (10150) *********************** 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 121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.802 Fit side-chains REVERT: A 91 LYS cc_start: 0.7460 (mttt) cc_final: 0.7244 (mttm) REVERT: A 1043 SER cc_start: 0.7419 (m) cc_final: 0.6842 (p) REVERT: A 1045 GLN cc_start: 0.7046 (mp10) cc_final: 0.6747 (mp10) REVERT: A 1053 MET cc_start: 0.7525 (mtp) cc_final: 0.7299 (mtt) REVERT: A 1125 MET cc_start: 0.7990 (mmm) cc_final: 0.7547 (mmm) REVERT: A 1191 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.4312 (mmt180) REVERT: B 55 SER cc_start: 0.8047 (t) cc_final: 0.7548 (p) REVERT: B 100 MET cc_start: 0.4702 (pmm) cc_final: 0.4010 (ttp) REVERT: B 396 GLU cc_start: 0.8291 (tp30) cc_final: 0.8083 (tp30) REVERT: B 1016 GLU cc_start: 0.7538 (pt0) cc_final: 0.6932 (mt-10) REVERT: B 1045 GLN cc_start: 0.7261 (mp10) cc_final: 0.6919 (mp10) outliers start: 20 outliers final: 9 residues processed: 114 average time/residue: 1.2020 time to fit residues: 144.7368 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 : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 373 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 351 ASN B1158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121547 restraints weight = 7484.793| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.31 r_work: 0.3302 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7502 Z= 0.117 Angle : 0.525 7.436 10176 Z= 0.268 Chirality : 0.043 0.137 1119 Planarity : 0.004 0.040 1293 Dihedral : 10.859 101.843 1214 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.73 % Allowed : 11.03 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.30), residues: 841 helix: 1.42 (0.28), residues: 373 sheet: 0.48 (0.59), residues: 82 loop : -0.22 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 416 HIS 0.005 0.001 HIS B 987 PHE 0.028 0.002 PHE A 982 TYR 0.014 0.001 TYR B 937 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 7) link_NAG-ASN : angle 1.83946 ( 21) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 1.03946 ( 3) hydrogen bonds : bond 0.03977 ( 294) hydrogen bonds : angle 4.49719 ( 852) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.32879 ( 2) covalent geometry : bond 0.00260 ( 7493) covalent geometry : angle 0.51826 (10150) *********************** 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 125 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.797 Fit side-chains REVERT: A 91 LYS cc_start: 0.7458 (mttt) cc_final: 0.7234 (mttm) REVERT: A 325 ASP cc_start: 0.7627 (t0) cc_final: 0.7343 (t0) REVERT: A 1045 GLN cc_start: 0.6948 (mp10) cc_final: 0.6697 (mp10) REVERT: A 1053 MET cc_start: 0.7572 (mtp) cc_final: 0.7334 (mtt) REVERT: A 1191 ARG cc_start: 0.6747 (mtm-85) cc_final: 0.4261 (mmt180) REVERT: B 55 SER cc_start: 0.8000 (t) cc_final: 0.7567 (p) REVERT: B 94 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: B 100 MET cc_start: 0.4613 (pmm) cc_final: 0.3954 (ttp) REVERT: B 414 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: B 992 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: B 1002 MET cc_start: 0.8608 (mtp) cc_final: 0.8396 (mtm) REVERT: B 1016 GLU cc_start: 0.7565 (pt0) cc_final: 0.6912 (mt-10) REVERT: B 1045 GLN cc_start: 0.7354 (mp10) cc_final: 0.7029 (mp-120) outliers start: 22 outliers final: 8 residues processed: 122 average time/residue: 1.1515 time to fit residues: 148.9211 Evaluate side-chains 108 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 407 ASP Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1169 ARG Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 992 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3739 r_free = 0.3739 target = 0.147075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119521 restraints weight = 7606.858| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.30 r_work: 0.3276 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1431 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= 0.138 Angle : 0.548 7.429 10176 Z= 0.277 Chirality : 0.044 0.144 1119 Planarity : 0.004 0.038 1293 Dihedral : 10.818 101.505 1214 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.85 % Allowed : 12.02 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 841 helix: 1.40 (0.28), residues: 373 sheet: 0.44 (0.59), residues: 82 loop : -0.27 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 416 HIS 0.005 0.001 HIS B 987 PHE 0.028 0.002 PHE A 982 TYR 0.014 0.001 TYR B 937 ARG 0.003 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.81230 ( 21) link_BETA1-4 : bond 0.00358 ( 1) link_BETA1-4 : angle 1.10797 ( 3) hydrogen bonds : bond 0.03997 ( 294) hydrogen bonds : angle 4.41290 ( 852) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.22223 ( 2) covalent geometry : bond 0.00319 ( 7493) covalent geometry : angle 0.54204 (10150) *********************** 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 127 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.804 Fit side-chains REVERT: A 91 LYS cc_start: 0.7425 (mttt) cc_final: 0.7194 (mttm) REVERT: A 325 ASP cc_start: 0.7607 (t0) cc_final: 0.7320 (t0) REVERT: A 371 GLN cc_start: 0.7790 (mm110) cc_final: 0.7502 (mp-120) REVERT: A 1053 MET cc_start: 0.7517 (mtp) cc_final: 0.7295 (mtt) REVERT: A 1060 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5647 (mmm) REVERT: A 1191 ARG cc_start: 0.6703 (mtm-85) cc_final: 0.4214 (mmt180) REVERT: B 55 SER cc_start: 0.8035 (t) cc_final: 0.7574 (p) REVERT: B 94 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: B 100 MET cc_start: 0.4827 (pmm) cc_final: 0.3319 (tmt) REVERT: B 414 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: B 992 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: B 1016 GLU cc_start: 0.7554 (pt0) cc_final: 0.6892 (mt-10) REVERT: B 1045 GLN cc_start: 0.7254 (mp10) cc_final: 0.6948 (mp10) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 1.1918 time to fit residues: 152.4819 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 : 0.879 ------------------------------------------------------------------------------- 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 1060 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 94 GLN 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 414 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 48 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3740 r_free = 0.3740 target = 0.147121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119973 restraints weight = 7482.289| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.26 r_work: 0.3287 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7502 Z= 0.144 Angle : 0.557 7.371 10176 Z= 0.283 Chirality : 0.044 0.147 1119 Planarity : 0.004 0.038 1293 Dihedral : 10.864 101.965 1214 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.35 % Allowed : 12.89 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 841 helix: 1.42 (0.28), residues: 373 sheet: -0.11 (0.55), residues: 94 loop : -0.24 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 416 HIS 0.006 0.001 HIS B 987 PHE 0.028 0.002 PHE A 982 TYR 0.014 0.002 TYR B 937 ARG 0.002 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 7) link_NAG-ASN : angle 1.79172 ( 21) link_BETA1-4 : bond 0.00423 ( 1) link_BETA1-4 : angle 1.08794 ( 3) hydrogen bonds : bond 0.03968 ( 294) hydrogen bonds : angle 4.37592 ( 852) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.22866 ( 2) covalent geometry : bond 0.00335 ( 7493) covalent geometry : angle 0.55151 (10150) *********************** 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 128 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.864 Fit side-chains REVERT: A 91 LYS cc_start: 0.7482 (mttt) cc_final: 0.7252 (mttm) REVERT: A 325 ASP cc_start: 0.7644 (t0) cc_final: 0.7364 (t0) REVERT: A 1060 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5718 (mmm) REVERT: A 1191 ARG cc_start: 0.6737 (mtm-85) cc_final: 0.4240 (mmt180) REVERT: B 55 SER cc_start: 0.8044 (t) cc_final: 0.7574 (p) REVERT: B 94 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: B 100 MET cc_start: 0.4848 (pmm) cc_final: 0.3475 (tmt) REVERT: B 414 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: B 992 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 1016 GLU cc_start: 0.7526 (pt0) cc_final: 0.6890 (mt-10) REVERT: B 1045 GLN cc_start: 0.7251 (mp10) cc_final: 0.6963 (mp10) outliers start: 27 outliers final: 14 residues processed: 121 average time/residue: 1.1725 time to fit residues: 150.2293 Evaluate side-chains 117 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 953 VAL Chi-restraints excluded: chain A residue 976 GLU 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 94 GLN 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 414 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 38 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3740 r_free = 0.3740 target = 0.147106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119881 restraints weight = 7520.104| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.26 r_work: 0.3277 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1608 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= 0.143 Angle : 0.555 7.313 10176 Z= 0.281 Chirality : 0.044 0.148 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.895 102.285 1214 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.35 % Allowed : 13.01 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 841 helix: 1.39 (0.28), residues: 374 sheet: -0.12 (0.55), residues: 94 loop : -0.24 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 416 HIS 0.006 0.001 HIS B 987 PHE 0.028 0.002 PHE A 982 TYR 0.014 0.002 TYR B 937 ARG 0.002 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 7) link_NAG-ASN : angle 1.76835 ( 21) link_BETA1-4 : bond 0.00398 ( 1) link_BETA1-4 : angle 1.09617 ( 3) hydrogen bonds : bond 0.03940 ( 294) hydrogen bonds : angle 4.37562 ( 852) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.28856 ( 2) covalent geometry : bond 0.00332 ( 7493) covalent geometry : angle 0.54945 (10150) *********************** 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 130 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.797 Fit side-chains REVERT: A 325 ASP cc_start: 0.7663 (t0) cc_final: 0.7391 (t0) REVERT: A 1060 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5790 (mmm) REVERT: A 1112 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: A 1191 ARG cc_start: 0.6707 (mtm-85) cc_final: 0.4212 (mmt180) REVERT: B 55 SER cc_start: 0.8038 (t) cc_final: 0.7552 (p) REVERT: B 94 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: B 100 MET cc_start: 0.4958 (pmm) cc_final: 0.3548 (tmt) REVERT: B 414 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: B 992 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 1002 MET cc_start: 0.8630 (mtp) cc_final: 0.8407 (mtm) REVERT: B 1016 GLU cc_start: 0.7518 (pt0) cc_final: 0.6886 (mt-10) REVERT: B 1045 GLN cc_start: 0.7243 (mp10) cc_final: 0.6971 (mp10) outliers start: 27 outliers final: 15 residues processed: 124 average time/residue: 1.1840 time to fit residues: 155.1440 Evaluate side-chains 119 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 94 GLN 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 414 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 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 29 optimal weight: 0.0020 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3748 r_free = 0.3748 target = 0.147797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120292 restraints weight = 7491.086| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.29 r_work: 0.3297 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7502 Z= 0.130 Angle : 0.553 7.333 10176 Z= 0.280 Chirality : 0.043 0.151 1119 Planarity : 0.004 0.037 1293 Dihedral : 10.898 102.123 1214 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.22 % Allowed : 13.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 841 helix: 1.43 (0.28), residues: 374 sheet: -0.14 (0.55), residues: 94 loop : -0.22 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 416 HIS 0.007 0.001 HIS B 987 PHE 0.027 0.002 PHE A 982 TYR 0.014 0.001 TYR B 331 ARG 0.002 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 7) link_NAG-ASN : angle 1.75319 ( 21) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 1.07733 ( 3) hydrogen bonds : bond 0.03822 ( 294) hydrogen bonds : angle 4.35686 ( 852) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.31271 ( 2) covalent geometry : bond 0.00297 ( 7493) covalent geometry : angle 0.54752 (10150) *********************** 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 131 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.804 Fit side-chains REVERT: A 325 ASP cc_start: 0.7663 (t0) cc_final: 0.7386 (t0) REVERT: A 371 GLN cc_start: 0.7819 (mm110) cc_final: 0.7549 (mp-120) REVERT: A 1060 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5780 (mmm) REVERT: A 1191 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.4259 (mmt180) REVERT: B 55 SER cc_start: 0.8064 (t) cc_final: 0.7572 (p) REVERT: B 94 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: B 100 MET cc_start: 0.4947 (pmm) cc_final: 0.3590 (tmt) REVERT: B 414 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: B 992 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 1002 MET cc_start: 0.8652 (mtp) cc_final: 0.8434 (mtm) REVERT: B 1016 GLU cc_start: 0.7520 (pt0) cc_final: 0.6854 (mt-10) REVERT: B 1045 GLN cc_start: 0.7246 (mp10) cc_final: 0.6949 (mp-120) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 1.1713 time to fit residues: 153.5391 Evaluate side-chains 120 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 953 VAL Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 992 GLN 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 94 GLN 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 414 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 68 optimal weight: 0.3980 chunk 39 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3761 r_free = 0.3761 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121834 restraints weight = 7546.102| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.26 r_work: 0.3304 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1715 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= 0.119 Angle : 0.544 7.484 10176 Z= 0.274 Chirality : 0.043 0.150 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.844 100.595 1214 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.85 % Allowed : 14.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 841 helix: 1.52 (0.28), residues: 373 sheet: 0.27 (0.58), residues: 84 loop : -0.27 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 416 HIS 0.008 0.001 HIS B 987 PHE 0.027 0.002 PHE A 982 TYR 0.014 0.001 TYR B 937 ARG 0.001 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 1.72699 ( 21) link_BETA1-4 : bond 0.00385 ( 1) link_BETA1-4 : angle 1.05650 ( 3) hydrogen bonds : bond 0.03671 ( 294) hydrogen bonds : angle 4.31407 ( 852) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.31724 ( 2) covalent geometry : bond 0.00269 ( 7493) covalent geometry : angle 0.53881 (10150) *********************** 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 126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.876 Fit side-chains REVERT: A 325 ASP cc_start: 0.7594 (t0) cc_final: 0.7345 (t0) REVERT: A 371 GLN cc_start: 0.7795 (mm110) cc_final: 0.7531 (mp-120) REVERT: A 1060 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5802 (mmm) REVERT: A 1191 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.4185 (mmt180) REVERT: B 55 SER cc_start: 0.8046 (t) cc_final: 0.7551 (p) REVERT: B 94 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: B 414 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: B 992 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: B 1002 MET cc_start: 0.8642 (mtp) cc_final: 0.8416 (mtm) REVERT: B 1016 GLU cc_start: 0.7536 (pt0) cc_final: 0.6870 (mt-10) REVERT: B 1045 GLN cc_start: 0.7243 (mp10) cc_final: 0.6969 (mp-120) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 1.2071 time to fit residues: 154.8585 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 : 0.894 ------------------------------------------------------------------------------- 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 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 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 94 GLN 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 414 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 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3745 r_free = 0.3745 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120311 restraints weight = 7548.822| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.26 r_work: 0.3290 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7502 Z= 0.152 Angle : 0.583 8.006 10176 Z= 0.294 Chirality : 0.044 0.162 1119 Planarity : 0.004 0.035 1293 Dihedral : 10.852 101.093 1214 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.60 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 841 helix: 1.46 (0.28), residues: 373 sheet: -0.15 (0.55), residues: 94 loop : -0.30 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 416 HIS 0.009 0.001 HIS B 987 PHE 0.027 0.002 PHE A 982 TYR 0.015 0.002 TYR B 331 ARG 0.002 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 7) link_NAG-ASN : angle 1.74327 ( 21) link_BETA1-4 : bond 0.00370 ( 1) link_BETA1-4 : angle 1.05328 ( 3) hydrogen bonds : bond 0.03895 ( 294) hydrogen bonds : angle 4.38594 ( 852) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.26671 ( 2) covalent geometry : bond 0.00355 ( 7493) covalent geometry : angle 0.57837 (10150) *********************** 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: 21 poor density : 102 time to evaluate : 0.838 Fit side-chains REVERT: A 325 ASP cc_start: 0.7709 (t0) cc_final: 0.7464 (t0) REVERT: A 371 GLN cc_start: 0.7800 (mm110) cc_final: 0.7563 (mp-120) REVERT: A 1060 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5847 (mmm) REVERT: A 1191 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.4223 (mmt180) REVERT: B 55 SER cc_start: 0.8072 (t) cc_final: 0.7578 (p) REVERT: B 94 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 100 MET cc_start: 0.4786 (pmm) cc_final: 0.4070 (OUTLIER) REVERT: B 414 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: B 992 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: B 1002 MET cc_start: 0.8656 (mtp) cc_final: 0.8442 (mtm) REVERT: B 1016 GLU cc_start: 0.7529 (pt0) cc_final: 0.6864 (mt-10) REVERT: B 1045 GLN cc_start: 0.7300 (mp10) cc_final: 0.7043 (mp10) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 1.1719 time to fit residues: 145.3086 Evaluate side-chains 117 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 94 GLN 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 414 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 20 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 17 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3760 r_free = 0.3760 target = 0.148753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121168 restraints weight = 7661.508| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.30 r_work: 0.3301 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7502 Z= 0.116 Angle : 0.562 8.163 10176 Z= 0.283 Chirality : 0.043 0.154 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.857 100.605 1214 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.23 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 841 helix: 1.55 (0.28), residues: 373 sheet: -0.22 (0.55), residues: 94 loop : -0.26 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 416 HIS 0.010 0.001 HIS B 987 PHE 0.026 0.001 PHE A 982 TYR 0.014 0.001 TYR B 331 ARG 0.001 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 1.70482 ( 21) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 1.01083 ( 3) hydrogen bonds : bond 0.03616 ( 294) hydrogen bonds : angle 4.35269 ( 852) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.34925 ( 2) covalent geometry : bond 0.00260 ( 7493) covalent geometry : angle 0.55738 (10150) ********************** 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 120 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.916 Fit side-chains REVERT: A 325 ASP cc_start: 0.7596 (t0) cc_final: 0.7338 (t0) REVERT: A 371 GLN cc_start: 0.7788 (mm110) cc_final: 0.7556 (mp-120) REVERT: A 1021 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8252 (mt0) REVERT: A 1060 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5818 (mmm) REVERT: A 1191 ARG cc_start: 0.6703 (mtm-85) cc_final: 0.4189 (mmt180) REVERT: B 55 SER cc_start: 0.8045 (t) cc_final: 0.7561 (p) REVERT: B 94 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: B 100 MET cc_start: 0.4788 (pmm) cc_final: 0.4156 (ttp) REVERT: B 414 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: B 992 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: B 1002 MET cc_start: 0.8649 (mtp) cc_final: 0.8422 (mtm) REVERT: B 1016 GLU cc_start: 0.7520 (pt0) cc_final: 0.6843 (mt-10) REVERT: B 1045 GLN cc_start: 0.7267 (mp10) cc_final: 0.7007 (mp10) REVERT: B 1125 MET cc_start: 0.8022 (mtp) cc_final: 0.7737 (mtp) outliers start: 18 outliers final: 11 residues processed: 114 average time/residue: 1.1916 time to fit residues: 143.9052 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 : 0.909 ------------------------------------------------------------------------------- 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 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 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 414 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 31 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3758 r_free = 0.3758 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121580 restraints weight = 7503.828| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.26 r_work: 0.3311 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7502 Z= 0.128 Angle : 0.570 9.114 10176 Z= 0.287 Chirality : 0.043 0.161 1119 Planarity : 0.004 0.036 1293 Dihedral : 10.830 100.207 1214 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.98 % Allowed : 16.48 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.30), residues: 841 helix: 1.52 (0.28), residues: 373 sheet: -0.25 (0.54), residues: 94 loop : -0.27 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 416 HIS 0.011 0.001 HIS B 987 PHE 0.026 0.002 PHE A 982 TYR 0.014 0.001 TYR B 331 ARG 0.001 0.000 ARG A 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 7) link_NAG-ASN : angle 1.69133 ( 21) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 1.05026 ( 3) hydrogen bonds : bond 0.03717 ( 294) hydrogen bonds : angle 4.36257 ( 852) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.29490 ( 2) covalent geometry : bond 0.00292 ( 7493) covalent geometry : angle 0.56517 (10150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8787.26 seconds wall clock time: 151 minutes 21.25 seconds (9081.25 seconds total)