Starting phenix.real_space_refine on Tue Feb 11 13:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.map" model { file = "/net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xgr_33187/02_2025/7xgr_33187.cif" } resolution = 2.6 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1823 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2764 2.51 5 N 749 2.21 5 O 807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4340 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.51, per 1000 atoms: 0.81 Number of scatterers: 4340 At special positions: 0 Unit cell: (95.23, 104.86, 146.59, 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 20 16.00 O 807 8.00 N 749 7.00 C 2764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 536.0 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1046 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 859 through 875 removed outlier: 3.994A pdb=" N GLN A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.298A pdb=" N GLU A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 890' Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.576A pdb=" N THR A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 893 through 898' Processing helix chain 'A' and resid 898 through 910 removed outlier: 3.721A pdb=" N ILE A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.857A pdb=" N TRP A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 930 " --> pdb=" O MET A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 943 removed outlier: 3.656A pdb=" N GLN A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 953 Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 975 removed outlier: 3.516A pdb=" N GLU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 988 Processing helix chain 'A' and resid 990 through 1000 Processing helix chain 'A' and resid 1003 through 1015 Processing helix chain 'A' and resid 1019 through 1036 removed outlier: 3.688A pdb=" N ASP A1036 " --> pdb=" O VAL A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.626A pdb=" N LYS A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1061 removed outlier: 3.612A pdb=" N ALA A1055 " --> pdb=" O CYS A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1078 removed outlier: 3.571A pdb=" N VAL A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1096 removed outlier: 3.513A pdb=" N SER A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1108 removed outlier: 3.610A pdb=" N GLN A1105 " --> pdb=" O TRP A1101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1137 removed outlier: 3.661A pdb=" N LEU A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A1134 " --> pdb=" O HIS A1130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1136 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1169 Processing helix chain 'A' and resid 1173 through 1185 removed outlier: 3.884A pdb=" N GLN A1177 " --> pdb=" O PRO A1173 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A1178 " --> pdb=" O GLU A1174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A1185 " --> pdb=" O GLN A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1217 removed outlier: 3.758A pdb=" N LEU A1201 " --> pdb=" O ALA A1197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A1207 " --> pdb=" O HIS A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1237 Processing helix chain 'A' and resid 1239 through 1251 removed outlier: 3.679A pdb=" N TYR A1247 " --> pdb=" O MET A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1259 removed outlier: 3.609A pdb=" N LEU A1258 " --> pdb=" O CYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1293 Processing helix chain 'A' and resid 1349 through 1354 removed outlier: 3.743A pdb=" N LEU A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 4.188A pdb=" N GLU A1358 " --> pdb=" O THR A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1389 removed outlier: 3.598A pdb=" N GLU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1382 " --> pdb=" O GLN A1378 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A1389 " --> pdb=" O ILE A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1443 Processing helix chain 'A' and resid 1444 through 1448 removed outlier: 3.525A pdb=" N PHE A1448 " --> pdb=" O MET A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1455 removed outlier: 3.956A pdb=" N LYS A1453 " --> pdb=" O PRO A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1472 removed outlier: 3.584A pdb=" N LEU A1467 " --> pdb=" O CYS A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1495 removed outlier: 3.958A pdb=" N ASN A1495 " --> pdb=" O GLN A1491 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 812 1.33 - 1.45: 1107 1.45 - 1.57: 2487 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 4435 Sorted by residual: bond pdb=" CA ILE A1470 " pdb=" C ILE A1470 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.22e-02 6.72e+03 8.67e+00 bond pdb=" C ILE A1470 " pdb=" O ILE A1470 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.13e-02 7.83e+03 8.16e+00 bond pdb=" CA PHE A1457 " pdb=" CB PHE A1457 " ideal model delta sigma weight residual 1.535 1.503 0.032 1.21e-02 6.83e+03 7.16e+00 bond pdb=" N PHE A1457 " pdb=" CA PHE A1457 " ideal model delta sigma weight residual 1.453 1.433 0.020 9.20e-03 1.18e+04 4.77e+00 bond pdb=" C LEU A1468 " pdb=" O LEU A1468 " ideal model delta sigma weight residual 1.237 1.212 0.024 1.16e-02 7.43e+03 4.44e+00 ... (remaining 4430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 5857 1.88 - 3.76: 114 3.76 - 5.64: 21 5.64 - 7.52: 9 7.52 - 9.41: 4 Bond angle restraints: 6005 Sorted by residual: angle pdb=" N ILE A 908 " pdb=" CA ILE A 908 " pdb=" C ILE A 908 " ideal model delta sigma weight residual 113.71 105.60 8.11 9.50e-01 1.11e+00 7.28e+01 angle pdb=" N LYS A 911 " pdb=" CA LYS A 911 " pdb=" C LYS A 911 " ideal model delta sigma weight residual 108.63 99.22 9.41 1.60e+00 3.91e-01 3.46e+01 angle pdb=" CA GLU A1112 " pdb=" CB GLU A1112 " pdb=" CG GLU A1112 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA ARG A1294 " pdb=" CB ARG A1294 " pdb=" CG ARG A1294 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N ILE A1186 " pdb=" CA ILE A1186 " pdb=" C ILE A1186 " ideal model delta sigma weight residual 109.37 114.18 -4.81 1.35e+00 5.49e-01 1.27e+01 ... (remaining 6000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2218 17.17 - 34.35: 295 34.35 - 51.52: 114 51.52 - 68.69: 21 68.69 - 85.86: 11 Dihedral angle restraints: 2659 sinusoidal: 1055 harmonic: 1604 Sorted by residual: dihedral pdb=" CA GLY A 912 " pdb=" C GLY A 912 " pdb=" N HIS A 913 " pdb=" CA HIS A 913 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP A 907 " pdb=" C ASP A 907 " pdb=" N ILE A 908 " pdb=" CA ILE A 908 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU A 915 " pdb=" C GLU A 915 " pdb=" N ASN A 916 " pdb=" CA ASN A 916 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 607 0.062 - 0.125: 59 0.125 - 0.187: 0 0.187 - 0.250: 1 0.250 - 0.312: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA ARG A1471 " pdb=" N ARG A1471 " pdb=" C ARG A1471 " pdb=" CB ARG A1471 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA LYS A 911 " pdb=" N LYS A 911 " pdb=" C LYS A 911 " pdb=" CB LYS A 911 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA GLU A1112 " pdb=" N GLU A1112 " pdb=" C GLU A1112 " pdb=" CB GLU A1112 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 666 not shown) Planarity restraints: 767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1467 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU A1467 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A1467 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A1468 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1456 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C PRO A1456 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO A1456 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A1457 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1112 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C GLU A1112 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A1112 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A1113 " 0.009 2.00e-02 2.50e+03 ... (remaining 764 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1070 2.79 - 3.32: 4306 3.32 - 3.84: 6857 3.84 - 4.37: 8337 4.37 - 4.90: 13665 Nonbonded interactions: 34235 Sorted by model distance: nonbonded pdb=" NZ LYS A 999 " pdb=" OD2 ASP A1024 " model vdw 2.259 3.120 nonbonded pdb=" O SER A1239 " pdb=" OG SER A1239 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A1247 " pdb=" O LEU A1276 " model vdw 2.277 3.040 nonbonded pdb=" O SER A1142 " pdb=" OG SER A1142 " model vdw 2.300 3.040 nonbonded pdb=" O ASP A1264 " pdb=" NE2 GLN A1266 " model vdw 2.308 3.120 ... (remaining 34230 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=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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.390 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:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.004 0.044 4435 Z= 0.259 Angle : 0.706 9.406 6005 Z= 0.418 Chirality : 0.040 0.312 669 Planarity : 0.004 0.035 767 Dihedral : 18.877 85.862 1613 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.17 % Allowed : 27.17 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.38), residues: 536 helix: 0.25 (0.27), residues: 396 sheet: None (None), residues: 0 loop : -1.18 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1455 HIS 0.003 0.001 HIS A1473 PHE 0.007 0.001 PHE A1448 TYR 0.012 0.001 TYR A1053 ARG 0.004 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 1352 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8676 (tmm) outliers start: 10 outliers final: 5 residues processed: 33 average time/residue: 1.3039 time to fit residues: 45.0368 Evaluate side-chains 23 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1161 THR Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1352 MET Chi-restraints excluded: chain A residue 1377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.097379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075425 restraints weight = 11347.063| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.13 r_work: 0.3258 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4435 Z= 0.281 Angle : 0.634 12.137 6005 Z= 0.318 Chirality : 0.038 0.142 669 Planarity : 0.004 0.036 767 Dihedral : 5.444 41.226 592 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.26 % Allowed : 25.87 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.39), residues: 536 helix: 1.04 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.85 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1455 HIS 0.004 0.001 HIS A1388 PHE 0.008 0.001 PHE A1273 TYR 0.015 0.001 TYR A1026 ARG 0.002 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 909 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: A 1237 SER cc_start: 0.9165 (t) cc_final: 0.8788 (p) outliers start: 15 outliers final: 5 residues processed: 36 average time/residue: 1.0955 time to fit residues: 41.4459 Evaluate side-chains 23 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 909 GLU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1388 HIS Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077123 restraints weight = 11261.747| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.10 r_work: 0.3287 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4435 Z= 0.206 Angle : 0.565 11.355 6005 Z= 0.284 Chirality : 0.036 0.143 669 Planarity : 0.004 0.037 767 Dihedral : 4.550 27.535 584 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.26 % Allowed : 25.65 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.38), residues: 536 helix: 1.34 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.75 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1455 HIS 0.003 0.001 HIS A1388 PHE 0.007 0.001 PHE A1457 TYR 0.010 0.001 TYR A1026 ARG 0.002 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.506 Fit side-chains REVERT: A 944 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: A 1181 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: A 1237 SER cc_start: 0.9101 (t) cc_final: 0.8819 (p) outliers start: 15 outliers final: 5 residues processed: 34 average time/residue: 1.1070 time to fit residues: 39.7230 Evaluate side-chains 23 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.098490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076375 restraints weight = 11307.485| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.16 r_work: 0.3276 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4435 Z= 0.232 Angle : 0.584 10.769 6005 Z= 0.290 Chirality : 0.037 0.141 669 Planarity : 0.004 0.037 767 Dihedral : 4.545 27.569 584 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.13 % Allowed : 24.57 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.38), residues: 536 helix: 1.42 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.64 (0.66), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1455 HIS 0.004 0.001 HIS A1388 PHE 0.007 0.001 PHE A1356 TYR 0.009 0.001 TYR A1282 ARG 0.002 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 20 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: A 1237 SER cc_start: 0.9093 (t) cc_final: 0.8805 (p) outliers start: 19 outliers final: 9 residues processed: 37 average time/residue: 1.0764 time to fit residues: 41.9326 Evaluate side-chains 28 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1161 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1388 HIS Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.098738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076593 restraints weight = 11322.295| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.20 r_work: 0.3275 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 0.033 4435 Z= 0.216 Angle : 0.575 9.978 6005 Z= 0.285 Chirality : 0.036 0.140 669 Planarity : 0.004 0.037 767 Dihedral : 4.477 28.289 584 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.70 % Allowed : 23.26 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.38), residues: 536 helix: 1.54 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.57 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1455 HIS 0.003 0.001 HIS A1388 PHE 0.007 0.001 PHE A1356 TYR 0.010 0.001 TYR A1282 ARG 0.002 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 17 time to evaluate : 0.483 Fit side-chains REVERT: A 944 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: A 1181 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: A 1237 SER cc_start: 0.9104 (t) cc_final: 0.8816 (p) outliers start: 17 outliers final: 8 residues processed: 32 average time/residue: 1.1631 time to fit residues: 39.1376 Evaluate side-chains 28 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1161 THR Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.078975 restraints weight = 11069.083| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.15 r_work: 0.3321 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4435 Z= 0.147 Angle : 0.541 9.402 6005 Z= 0.267 Chirality : 0.035 0.140 669 Planarity : 0.003 0.035 767 Dihedral : 4.276 27.707 584 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.48 % Allowed : 23.26 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.38), residues: 536 helix: 1.78 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.55 (0.65), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.003 0.001 HIS A1257 PHE 0.006 0.001 PHE A1457 TYR 0.010 0.001 TYR A1282 ARG 0.001 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: A 1178 GLU cc_start: 0.8707 (mp0) cc_final: 0.8506 (mp0) REVERT: A 1222 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: A 1237 SER cc_start: 0.9087 (t) cc_final: 0.8844 (p) REVERT: A 1255 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8205 (t) outliers start: 16 outliers final: 5 residues processed: 37 average time/residue: 1.5177 time to fit residues: 58.2946 Evaluate side-chains 26 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.099921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.077760 restraints weight = 11223.572| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.19 r_work: 0.3297 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4435 Z= 0.197 Angle : 0.577 9.129 6005 Z= 0.287 Chirality : 0.036 0.139 669 Planarity : 0.004 0.034 767 Dihedral : 4.303 27.467 584 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.39 % Allowed : 25.00 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.38), residues: 536 helix: 1.81 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.54 (0.64), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.003 0.001 HIS A1111 PHE 0.006 0.001 PHE A1457 TYR 0.009 0.001 TYR A1282 ARG 0.001 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.513 Fit side-chains REVERT: A 944 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: A 1178 GLU cc_start: 0.8850 (mp0) cc_final: 0.8541 (mp0) REVERT: A 1222 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: A 1237 SER cc_start: 0.9100 (t) cc_final: 0.8818 (p) outliers start: 11 outliers final: 5 residues processed: 32 average time/residue: 1.2151 time to fit residues: 40.8301 Evaluate side-chains 25 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1161 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077447 restraints weight = 11018.407| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.19 r_work: 0.3290 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4435 Z= 0.208 Angle : 0.587 8.835 6005 Z= 0.292 Chirality : 0.036 0.139 669 Planarity : 0.003 0.030 767 Dihedral : 4.320 27.086 584 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.83 % Allowed : 24.78 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.38), residues: 536 helix: 1.81 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.56 (0.65), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.003 0.001 HIS A1111 PHE 0.006 0.001 PHE A1356 TYR 0.009 0.001 TYR A1282 ARG 0.001 0.000 ARG A1351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (mt-10) REVERT: A 1178 GLU cc_start: 0.8852 (mp0) cc_final: 0.8513 (mp0) REVERT: A 1222 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: A 1237 SER cc_start: 0.9102 (t) cc_final: 0.8809 (p) REVERT: A 1255 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8253 (t) outliers start: 13 outliers final: 6 residues processed: 32 average time/residue: 1.0733 time to fit residues: 36.2912 Evaluate side-chains 27 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1161 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078339 restraints weight = 11260.865| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.20 r_work: 0.3309 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4435 Z= 0.174 Angle : 0.586 8.608 6005 Z= 0.286 Chirality : 0.036 0.140 669 Planarity : 0.003 0.029 767 Dihedral : 4.228 27.229 584 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.17 % Allowed : 25.65 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.38), residues: 536 helix: 1.89 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.54 (0.65), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.002 0.001 HIS A1111 PHE 0.006 0.001 PHE A1457 TYR 0.010 0.001 TYR A1282 ARG 0.001 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: A 1178 GLU cc_start: 0.8818 (mp0) cc_final: 0.8531 (mp0) REVERT: A 1222 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: A 1237 SER cc_start: 0.9106 (t) cc_final: 0.8831 (p) outliers start: 10 outliers final: 7 residues processed: 31 average time/residue: 1.1959 time to fit residues: 39.0082 Evaluate side-chains 27 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077666 restraints weight = 10950.246| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.20 r_work: 0.3295 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4435 Z= 0.199 Angle : 0.590 8.592 6005 Z= 0.289 Chirality : 0.036 0.139 669 Planarity : 0.003 0.030 767 Dihedral : 4.258 26.840 584 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.52 % Allowed : 26.52 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.38), residues: 536 helix: 1.85 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.46 (0.66), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1455 HIS 0.003 0.001 HIS A1473 PHE 0.006 0.001 PHE A1457 TYR 0.009 0.001 TYR A1282 ARG 0.001 0.000 ARG A1471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: A 1178 GLU cc_start: 0.8855 (mp0) cc_final: 0.8566 (mp0) REVERT: A 1237 SER cc_start: 0.9105 (t) cc_final: 0.8823 (p) outliers start: 7 outliers final: 7 residues processed: 25 average time/residue: 1.2614 time to fit residues: 33.2704 Evaluate side-chains 26 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.0030 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.100543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078093 restraints weight = 11079.588| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.22 r_work: 0.3306 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4435 Z= 0.171 Angle : 0.584 9.117 6005 Z= 0.283 Chirality : 0.035 0.139 669 Planarity : 0.003 0.030 767 Dihedral : 4.216 26.991 584 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.96 % Allowed : 26.09 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.38), residues: 536 helix: 1.88 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.46 (0.65), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.002 0.001 HIS A1111 PHE 0.006 0.001 PHE A1457 TYR 0.009 0.001 TYR A1282 ARG 0.001 0.000 ARG A 942 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.07 seconds wall clock time: 68 minutes 31.04 seconds (4111.04 seconds total)