Starting phenix.real_space_refine on Wed Sep 17 19:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5z_13847/09_2025/7q5z_13847.map" } resolution = 3.25 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= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6709 2.51 5 N 1719 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10489 Classifications: {'peptide': 1344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 70, 'TRANS': 1272} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.51, per 1000 atoms: 0.24 Number of scatterers: 10489 At special positions: 0 Unit cell: (87.2329, 106.004, 141.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2009 8.00 N 1719 7.00 C 6709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1453 " 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 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 424.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 16.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 365 through 369 removed outlier: 4.164A pdb=" N ASP A 368 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 4.100A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 973 through 977 removed outlier: 3.755A pdb=" N VAL A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 991 removed outlier: 3.652A pdb=" N ILE A 982 " --> pdb=" O PHE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1014 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1055 through 1069 removed outlier: 3.900A pdb=" N ILE A1059 " --> pdb=" O ASP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1109 removed outlier: 3.531A pdb=" N GLY A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1133 through 1147 removed outlier: 3.737A pdb=" N ALA A1147 " --> pdb=" O ILE A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 3.997A pdb=" N ILE A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 removed outlier: 3.689A pdb=" N GLU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.602A pdb=" N LYS A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1255 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.962A pdb=" N ARG A1283 " --> pdb=" O SER A1280 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1284 " --> pdb=" O VAL A1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1284' Processing helix chain 'A' and resid 1380 through 1387 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 56 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.487A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 285 removed outlier: 6.517A pdb=" N ALA A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A 317 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN A 255 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 315 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 257 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A 313 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS A 259 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 311 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS A 261 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.513A pdb=" N VAL A 470 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AB3, first strand: chain 'A' and resid 499 through 501 removed outlier: 5.792A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB5, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB6, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 removed outlier: 3.644A pdb=" N THR A 811 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 795 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 809 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 832 through 836 Processing sheet with id=AB9, first strand: chain 'A' and resid 799 through 801 removed outlier: 6.269A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC2, first strand: chain 'A' and resid 908 through 913 removed outlier: 3.880A pdb=" N TYR A1309 " --> pdb=" O LEU A 949 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 921 through 930 removed outlier: 4.485A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1164 through 1167 Processing sheet with id=AC5, first strand: chain 'A' and resid 1327 through 1332 Processing sheet with id=AC6, first strand: chain 'A' and resid 1393 through 1396 removed outlier: 4.014A pdb=" N LYS A1393 " --> pdb=" O TYR A1404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A1432 " --> pdb=" O LYS A1370 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1134 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: 2.41 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3209 1.34 - 1.46: 2476 1.46 - 1.58: 4958 1.58 - 1.71: 1 1.71 - 1.83: 79 Bond restraints: 10723 Sorted by residual: bond pdb=" CA ASP A1113 " pdb=" C ASP A1113 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.41e-02 5.03e+03 7.95e+00 bond pdb=" N ASP A 367 " pdb=" CA ASP A 367 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" C SER A1343 " pdb=" N PRO A1344 " ideal model delta sigma weight residual 1.334 1.386 -0.053 2.34e-02 1.83e+03 5.04e+00 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA MET A1378 " pdb=" CB MET A1378 " ideal model delta sigma weight residual 1.513 1.561 -0.048 2.59e-02 1.49e+03 3.38e+00 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 14385 3.64 - 7.28: 143 7.28 - 10.92: 38 10.92 - 14.56: 4 14.56 - 18.20: 1 Bond angle restraints: 14571 Sorted by residual: angle pdb=" N ILE A 760 " pdb=" CA ILE A 760 " pdb=" C ILE A 760 " ideal model delta sigma weight residual 113.47 106.82 6.65 1.01e+00 9.80e-01 4.34e+01 angle pdb=" CB MET A1087 " pdb=" CG MET A1087 " pdb=" SD MET A1087 " ideal model delta sigma weight residual 112.70 130.90 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" N GLU A1007 " pdb=" CA GLU A1007 " pdb=" CB GLU A1007 " ideal model delta sigma weight residual 110.40 119.96 -9.56 1.63e+00 3.76e-01 3.44e+01 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.73e+01 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5952 17.63 - 35.25: 416 35.25 - 52.88: 68 52.88 - 70.51: 15 70.51 - 88.13: 8 Dihedral angle restraints: 6459 sinusoidal: 2552 harmonic: 3907 Sorted by residual: dihedral pdb=" CA PHE A1235 " pdb=" C PHE A1235 " pdb=" N SER A1236 " pdb=" CA SER A1236 " ideal model delta harmonic sigma weight residual 180.00 -148.90 -31.10 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ALA A1086 " pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LYS A1088 " pdb=" C LYS A1088 " pdb=" N GLY A1089 " pdb=" CA GLY A1089 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 6456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1517 0.109 - 0.217: 133 0.217 - 0.326: 6 0.326 - 0.435: 1 0.435 - 0.544: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB VAL A 594 " pdb=" CA VAL A 594 " pdb=" CG1 VAL A 594 " pdb=" CG2 VAL A 594 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1656 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 84 " -0.102 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO A 85 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " 0.040 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR A1142 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1113 " 0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" CG ASP A1113 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASP A1113 " 0.028 2.00e-02 2.50e+03 pdb=" OD2 ASP A1113 " 0.026 2.00e-02 2.50e+03 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 9 2.38 - 3.01: 5119 3.01 - 3.64: 15503 3.64 - 4.27: 23295 4.27 - 4.90: 39032 Nonbonded interactions: 82958 Sorted by model distance: nonbonded pdb=" SG CYS A 970 " pdb=" CD GLN A 973 " model vdw 1.750 3.630 nonbonded pdb=" O THR A1038 " pdb=" OG1 THR A1042 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR A 58 " pdb=" O LYS A 61 " model vdw 2.337 3.040 nonbonded pdb=" OE1 GLU A 972 " pdb=" OH TYR A1439 " model vdw 2.352 3.040 nonbonded pdb=" O PRO A1377 " pdb=" OG1 THR A1381 " model vdw 2.359 3.040 ... (remaining 82953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.780 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.005 0.100 10734 Z= 0.221 Angle : 1.004 18.201 14593 Z= 0.517 Chirality : 0.062 0.544 1659 Planarity : 0.008 0.151 1870 Dihedral : 12.761 88.132 3916 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.62 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.07 (0.21), residues: 1332 helix: -2.57 (0.26), residues: 211 sheet: 0.06 (0.23), residues: 526 loop : -2.25 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.100 0.003 TYR A1142 PHE 0.028 0.003 PHE A1040 TRP 0.013 0.002 TRP A1224 HIS 0.002 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00473 (10723) covalent geometry : angle 1.00318 (14571) SS BOND : bond 0.00228 ( 11) SS BOND : angle 1.49900 ( 22) hydrogen bonds : bond 0.12881 ( 396) hydrogen bonds : angle 6.67765 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 PHE cc_start: 0.8053 (p90) cc_final: 0.7606 (p90) REVERT: A 523 THR cc_start: 0.7805 (p) cc_final: 0.7490 (p) REVERT: A 531 ASP cc_start: 0.8375 (p0) cc_final: 0.7609 (p0) REVERT: A 988 LEU cc_start: 0.8280 (mt) cc_final: 0.7799 (mt) REVERT: A 1060 GLN cc_start: 0.6778 (tm-30) cc_final: 0.6452 (tm-30) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.0842 time to fit residues: 15.4850 Evaluate side-chains 86 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 HIS ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.154530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.120695 restraints weight = 25592.224| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 4.14 r_work: 0.3877 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10734 Z= 0.144 Angle : 0.620 11.520 14593 Z= 0.315 Chirality : 0.045 0.163 1659 Planarity : 0.005 0.084 1870 Dihedral : 5.013 46.358 1438 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.94 % Allowed : 6.48 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -1.47 (0.22), residues: 1332 helix: -1.14 (0.32), residues: 212 sheet: 0.14 (0.23), residues: 533 loop : -1.97 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 605 TYR 0.020 0.001 TYR A1436 PHE 0.016 0.001 PHE A 618 TRP 0.015 0.001 TRP A1224 HIS 0.003 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00334 (10723) covalent geometry : angle 0.61944 (14571) SS BOND : bond 0.00157 ( 11) SS BOND : angle 0.86798 ( 22) hydrogen bonds : bond 0.03635 ( 396) hydrogen bonds : angle 5.41919 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7255 (mpp) cc_final: 0.6886 (mmp) REVERT: A 531 ASP cc_start: 0.8537 (p0) cc_final: 0.7858 (p0) REVERT: A 1037 LEU cc_start: 0.8371 (tp) cc_final: 0.7988 (tp) REVERT: A 1060 GLN cc_start: 0.7002 (tm-30) cc_final: 0.6544 (tm-30) REVERT: A 1206 THR cc_start: 0.7227 (OUTLIER) cc_final: 0.5850 (m) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.0883 time to fit residues: 14.0172 Evaluate side-chains 94 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 HIS ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.154110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.120014 restraints weight = 25734.658| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 4.30 r_work: 0.3866 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10734 Z= 0.126 Angle : 0.581 8.595 14593 Z= 0.296 Chirality : 0.044 0.153 1659 Planarity : 0.004 0.064 1870 Dihedral : 4.596 24.564 1435 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 1.53 % Allowed : 8.18 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -1.14 (0.23), residues: 1332 helix: -0.39 (0.34), residues: 212 sheet: 0.27 (0.23), residues: 518 loop : -1.84 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.013 0.001 TYR A1436 PHE 0.019 0.001 PHE A 219 TRP 0.012 0.001 TRP A1224 HIS 0.003 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00297 (10723) covalent geometry : angle 0.58057 (14571) SS BOND : bond 0.00149 ( 11) SS BOND : angle 0.80815 ( 22) hydrogen bonds : bond 0.03436 ( 396) hydrogen bonds : angle 5.16317 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7190 (mpp) cc_final: 0.6823 (mmt) REVERT: A 531 ASP cc_start: 0.8539 (p0) cc_final: 0.7874 (p0) REVERT: A 1037 LEU cc_start: 0.8361 (tp) cc_final: 0.7851 (tp) REVERT: A 1060 GLN cc_start: 0.7024 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 1206 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.5559 (m) outliers start: 18 outliers final: 11 residues processed: 100 average time/residue: 0.0877 time to fit residues: 13.7378 Evaluate side-chains 97 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.0070 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.0060 chunk 29 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.152478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.118123 restraints weight = 25937.877| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.41 r_work: 0.3837 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10734 Z= 0.150 Angle : 0.604 13.136 14593 Z= 0.304 Chirality : 0.044 0.167 1659 Planarity : 0.004 0.056 1870 Dihedral : 4.553 24.883 1435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 1.71 % Allowed : 10.14 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -1.01 (0.23), residues: 1332 helix: -0.19 (0.34), residues: 212 sheet: 0.30 (0.23), residues: 518 loop : -1.74 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 97 TYR 0.015 0.001 TYR A1436 PHE 0.019 0.001 PHE A 219 TRP 0.016 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00359 (10723) covalent geometry : angle 0.60369 (14571) SS BOND : bond 0.00162 ( 11) SS BOND : angle 0.72889 ( 22) hydrogen bonds : bond 0.03361 ( 396) hydrogen bonds : angle 5.08042 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8395 (m-40) cc_final: 0.8005 (m-40) REVERT: A 192 MET cc_start: 0.7237 (mpp) cc_final: 0.6916 (mmt) REVERT: A 531 ASP cc_start: 0.8557 (p0) cc_final: 0.8109 (p0) REVERT: A 1037 LEU cc_start: 0.8399 (tp) cc_final: 0.7969 (tp) REVERT: A 1060 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6584 (tm-30) REVERT: A 1206 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.5623 (m) REVERT: A 1379 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8240 (pp20) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 0.0890 time to fit residues: 13.8013 Evaluate side-chains 98 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.152473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.118278 restraints weight = 25605.580| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 4.15 r_work: 0.3838 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10734 Z= 0.134 Angle : 0.586 11.146 14593 Z= 0.295 Chirality : 0.044 0.147 1659 Planarity : 0.004 0.051 1870 Dihedral : 4.486 24.448 1435 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.22 % Allowed : 11.25 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.93 (0.23), residues: 1332 helix: -0.05 (0.35), residues: 212 sheet: 0.30 (0.23), residues: 519 loop : -1.67 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 97 TYR 0.013 0.001 TYR A1436 PHE 0.019 0.001 PHE A 219 TRP 0.019 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00322 (10723) covalent geometry : angle 0.58541 (14571) SS BOND : bond 0.00134 ( 11) SS BOND : angle 0.70132 ( 22) hydrogen bonds : bond 0.03313 ( 396) hydrogen bonds : angle 4.98973 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8378 (m-40) cc_final: 0.7994 (m-40) REVERT: A 342 MET cc_start: 0.1899 (mmm) cc_final: 0.1696 (mmm) REVERT: A 531 ASP cc_start: 0.8589 (p0) cc_final: 0.8158 (p0) REVERT: A 1037 LEU cc_start: 0.8412 (tp) cc_final: 0.7987 (tp) REVERT: A 1060 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6518 (tm-30) REVERT: A 1206 THR cc_start: 0.6202 (OUTLIER) cc_final: 0.5367 (m) outliers start: 26 outliers final: 18 residues processed: 104 average time/residue: 0.0799 time to fit residues: 13.6205 Evaluate side-chains 102 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 123 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 ASN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.150448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115682 restraints weight = 25982.506| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 4.37 r_work: 0.3796 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 10734 Z= 0.180 Angle : 0.622 10.460 14593 Z= 0.313 Chirality : 0.045 0.162 1659 Planarity : 0.004 0.049 1870 Dihedral : 4.632 25.423 1435 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 2.13 % Allowed : 12.11 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.93 (0.23), residues: 1332 helix: -0.14 (0.35), residues: 213 sheet: 0.30 (0.23), residues: 513 loop : -1.61 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 592 TYR 0.039 0.002 TYR A1142 PHE 0.019 0.002 PHE A 219 TRP 0.021 0.002 TRP A 837 HIS 0.005 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00431 (10723) covalent geometry : angle 0.62230 (14571) SS BOND : bond 0.00191 ( 11) SS BOND : angle 0.69353 ( 22) hydrogen bonds : bond 0.03534 ( 396) hydrogen bonds : angle 5.06689 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8447 (m-40) cc_final: 0.8043 (m-40) REVERT: A 531 ASP cc_start: 0.8635 (p0) cc_final: 0.8182 (p0) REVERT: A 1037 LEU cc_start: 0.8513 (tp) cc_final: 0.8166 (tp) REVERT: A 1060 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 1206 THR cc_start: 0.6638 (OUTLIER) cc_final: 0.5821 (m) outliers start: 25 outliers final: 17 residues processed: 104 average time/residue: 0.0787 time to fit residues: 13.3488 Evaluate side-chains 102 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.0040 chunk 102 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.153124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.118944 restraints weight = 25531.050| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 4.44 r_work: 0.3858 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10734 Z= 0.109 Angle : 0.581 9.050 14593 Z= 0.290 Chirality : 0.044 0.156 1659 Planarity : 0.004 0.048 1870 Dihedral : 4.444 24.331 1435 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 1.71 % Allowed : 12.45 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.75 (0.23), residues: 1332 helix: 0.25 (0.36), residues: 213 sheet: 0.39 (0.24), residues: 514 loop : -1.58 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1122 TYR 0.017 0.001 TYR A1142 PHE 0.020 0.001 PHE A 219 TRP 0.017 0.001 TRP A 837 HIS 0.002 0.000 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00256 (10723) covalent geometry : angle 0.58056 (14571) SS BOND : bond 0.00398 ( 11) SS BOND : angle 0.77446 ( 22) hydrogen bonds : bond 0.03180 ( 396) hydrogen bonds : angle 4.84809 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8332 (m-40) cc_final: 0.7948 (m-40) REVERT: A 99 SER cc_start: 0.8147 (p) cc_final: 0.7823 (m) REVERT: A 531 ASP cc_start: 0.8592 (p0) cc_final: 0.8159 (p0) REVERT: A 953 MET cc_start: 0.7550 (mmm) cc_final: 0.7235 (mmp) REVERT: A 1037 LEU cc_start: 0.8348 (tp) cc_final: 0.7565 (tp) REVERT: A 1060 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 1116 MET cc_start: 0.7450 (mmp) cc_final: 0.7232 (mmp) REVERT: A 1206 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.5187 (m) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 0.0801 time to fit residues: 13.2606 Evaluate side-chains 101 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 91 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 122 optimal weight: 0.0000 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.152226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.117730 restraints weight = 25586.852| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 4.35 r_work: 0.3836 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10734 Z= 0.135 Angle : 0.617 17.245 14593 Z= 0.305 Chirality : 0.044 0.173 1659 Planarity : 0.004 0.047 1870 Dihedral : 4.400 24.635 1435 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 2.13 % Allowed : 12.70 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.74 (0.23), residues: 1332 helix: 0.12 (0.35), residues: 214 sheet: 0.40 (0.24), residues: 515 loop : -1.52 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 605 TYR 0.049 0.001 TYR A1142 PHE 0.020 0.001 PHE A 219 TRP 0.018 0.001 TRP A 837 HIS 0.003 0.000 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00324 (10723) covalent geometry : angle 0.61645 (14571) SS BOND : bond 0.00175 ( 11) SS BOND : angle 0.82450 ( 22) hydrogen bonds : bond 0.03261 ( 396) hydrogen bonds : angle 4.85319 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8326 (m-40) cc_final: 0.7934 (m-40) REVERT: A 99 SER cc_start: 0.8174 (p) cc_final: 0.7890 (m) REVERT: A 531 ASP cc_start: 0.8594 (p0) cc_final: 0.8141 (p0) REVERT: A 953 MET cc_start: 0.7768 (mmm) cc_final: 0.7334 (mmp) REVERT: A 1060 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 1206 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.5271 (m) outliers start: 25 outliers final: 21 residues processed: 103 average time/residue: 0.0802 time to fit residues: 13.3533 Evaluate side-chains 109 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.149603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.115010 restraints weight = 25791.519| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.18 r_work: 0.3784 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 10734 Z= 0.202 Angle : 0.662 16.765 14593 Z= 0.330 Chirality : 0.046 0.172 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.615 25.401 1435 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 2.39 % Allowed : 12.62 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.90 (0.23), residues: 1332 helix: -0.23 (0.34), residues: 215 sheet: 0.35 (0.24), residues: 513 loop : -1.58 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 807 TYR 0.060 0.002 TYR A1142 PHE 0.020 0.002 PHE A 219 TRP 0.023 0.002 TRP A 837 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00488 (10723) covalent geometry : angle 0.66211 (14571) SS BOND : bond 0.00353 ( 11) SS BOND : angle 0.77434 ( 22) hydrogen bonds : bond 0.03579 ( 396) hydrogen bonds : angle 5.07541 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8430 (m-40) cc_final: 0.8029 (m-40) REVERT: A 99 SER cc_start: 0.8137 (p) cc_final: 0.7866 (m) REVERT: A 531 ASP cc_start: 0.8603 (p0) cc_final: 0.8151 (p0) REVERT: A 1037 LEU cc_start: 0.8187 (tp) cc_final: 0.7471 (tp) REVERT: A 1206 THR cc_start: 0.6460 (OUTLIER) cc_final: 0.5408 (m) REVERT: A 1324 MET cc_start: 0.7052 (mmp) cc_final: 0.6639 (mmt) outliers start: 28 outliers final: 23 residues processed: 103 average time/residue: 0.0769 time to fit residues: 12.9434 Evaluate side-chains 109 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 121 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.117022 restraints weight = 25527.385| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.93 r_work: 0.3825 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10734 Z= 0.148 Angle : 0.635 16.370 14593 Z= 0.316 Chirality : 0.045 0.217 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.547 25.278 1435 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.22 % Allowed : 12.96 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.83 (0.23), residues: 1332 helix: 0.00 (0.35), residues: 214 sheet: 0.31 (0.24), residues: 516 loop : -1.53 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.014 0.001 TYR A1142 PHE 0.021 0.001 PHE A 219 TRP 0.019 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00356 (10723) covalent geometry : angle 0.63448 (14571) SS BOND : bond 0.00277 ( 11) SS BOND : angle 0.77192 ( 22) hydrogen bonds : bond 0.03377 ( 396) hydrogen bonds : angle 5.02006 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8363 (m-40) cc_final: 0.7968 (m-40) REVERT: A 99 SER cc_start: 0.8015 (p) cc_final: 0.7799 (m) REVERT: A 531 ASP cc_start: 0.8591 (p0) cc_final: 0.8138 (p0) REVERT: A 953 MET cc_start: 0.7586 (mmm) cc_final: 0.7097 (mmp) REVERT: A 1037 LEU cc_start: 0.8031 (tp) cc_final: 0.7488 (tp) REVERT: A 1206 THR cc_start: 0.6381 (OUTLIER) cc_final: 0.5254 (m) REVERT: A 1324 MET cc_start: 0.6940 (mmp) cc_final: 0.6557 (mmt) outliers start: 26 outliers final: 22 residues processed: 102 average time/residue: 0.0775 time to fit residues: 12.9926 Evaluate side-chains 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 35 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.151790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.117680 restraints weight = 25900.469| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 4.22 r_work: 0.3830 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10734 Z= 0.134 Angle : 0.623 16.109 14593 Z= 0.311 Chirality : 0.045 0.228 1659 Planarity : 0.004 0.047 1870 Dihedral : 4.460 25.071 1435 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.13 % Allowed : 12.96 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: -0.72 (0.23), residues: 1332 helix: 0.14 (0.35), residues: 213 sheet: 0.41 (0.24), residues: 508 loop : -1.48 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.018 0.001 TYR A1142 PHE 0.021 0.001 PHE A 219 TRP 0.017 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00323 (10723) covalent geometry : angle 0.62293 (14571) SS BOND : bond 0.00232 ( 11) SS BOND : angle 0.76429 ( 22) hydrogen bonds : bond 0.03367 ( 396) hydrogen bonds : angle 4.94929 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.26 seconds wall clock time: 60 minutes 12.37 seconds (3612.37 seconds total)