Starting phenix.real_space_refine on Sun Mar 10 23:51:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_33187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_33187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_33187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_33187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgr_33187/03_2024/7xgr_33187.pdb" } 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 Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A GLU 1158": "OE1" <-> "OE2" Residue "A GLU 1174": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1287": "OE1" <-> "OE2" Residue "A GLU 1350": "OE1" <-> "OE2" Residue "A GLU 1481": "OE1" <-> "OE2" Residue "A GLU 1488": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.62, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 1.60 Conformation dependent library (CDL) restraints added in 697.6 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: 0.48 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: 1.18 Time building geometry restraints manager: 1.76 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: 99.22 - 106.17: 94 106.17 - 113.12: 2421 113.12 - 120.07: 1556 120.07 - 127.02: 1871 127.02 - 133.97: 63 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 2.520 nonbonded pdb=" O SER A1239 " pdb=" OG SER A1239 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR A1247 " pdb=" O LEU A1276 " model vdw 2.277 2.440 nonbonded pdb=" O SER A1142 " pdb=" OG SER A1142 " model vdw 2.300 2.440 nonbonded pdb=" O ASP A1264 " pdb=" NE2 GLN A1266 " model vdw 2.308 2.520 ... (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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 6.590 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.570 Find NCS groups from input model: 0.120 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.493 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: 1.2675 time to fit residues: 43.7554 Evaluate side-chains 23 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 0.4980 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: 3.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4435 Z= 0.299 Angle : 0.632 12.202 6005 Z= 0.315 Chirality : 0.038 0.141 669 Planarity : 0.004 0.037 767 Dihedral : 5.561 47.044 592 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.48 % Allowed : 26.96 % Favored : 69.57 % 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: 0.90 (0.39), residues: 536 helix: 1.06 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.75 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1455 HIS 0.004 0.001 HIS A1388 PHE 0.008 0.001 PHE A1356 TYR 0.016 0.001 TYR A1026 ARG 0.003 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 fitting. rotamer outliers: 16 poor density : 21 time to evaluate : 0.435 Fit side-chains REVERT: A 909 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: A 1237 SER cc_start: 0.9149 (t) cc_final: 0.8839 (p) outliers start: 16 outliers final: 5 residues processed: 34 average time/residue: 0.9400 time to fit residues: 33.9441 Evaluate side-chains 22 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 16 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 1147 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4435 Z= 0.186 Angle : 0.551 11.406 6005 Z= 0.274 Chirality : 0.036 0.144 669 Planarity : 0.003 0.036 767 Dihedral : 4.502 28.001 584 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.48 % Allowed : 26.30 % Favored : 70.22 % 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: 1.41 (0.39), residues: 536 helix: 1.46 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.66 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1455 HIS 0.003 0.001 HIS A1388 PHE 0.006 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 36 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.517 Fit side-chains REVERT: A 909 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: A 944 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7800 (mt-10) outliers start: 16 outliers final: 5 residues processed: 33 average time/residue: 1.0590 time to fit residues: 36.9181 Evaluate side-chains 23 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 16 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 944 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1161 THR 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 48 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4435 Z= 0.212 Angle : 0.565 10.863 6005 Z= 0.276 Chirality : 0.036 0.141 669 Planarity : 0.003 0.037 767 Dihedral : 4.481 28.122 584 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.91 % Allowed : 26.30 % Favored : 69.78 % 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: 1.58 (0.39), residues: 536 helix: 1.56 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.53 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.003 0.001 HIS A1388 PHE 0.006 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 fitting. rotamer outliers: 18 poor density : 21 time to evaluate : 0.473 Fit side-chains REVERT: A 909 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: A 944 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7744 (mt-10) outliers start: 18 outliers final: 7 residues processed: 37 average time/residue: 0.9798 time to fit residues: 38.3129 Evaluate side-chains 26 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 909 GLU Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1102 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4435 Z= 0.180 Angle : 0.559 11.784 6005 Z= 0.271 Chirality : 0.035 0.141 669 Planarity : 0.003 0.037 767 Dihedral : 4.391 28.032 584 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.26 % Allowed : 26.96 % Favored : 69.78 % 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: 1.77 (0.39), residues: 536 helix: 1.70 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.49 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.002 0.001 HIS A 892 PHE 0.005 0.001 PHE A1457 TYR 0.010 0.001 TYR A1282 ARG 0.001 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 35 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 20 time to evaluate : 0.501 Fit side-chains REVERT: A 944 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: A 1172 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.7626 (t) outliers start: 15 outliers final: 8 residues processed: 33 average time/residue: 1.1241 time to fit residues: 39.0888 Evaluate side-chains 27 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 17 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 944 GLU 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 1172 THR 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 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 43 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4435 Z= 0.162 Angle : 0.553 11.456 6005 Z= 0.271 Chirality : 0.035 0.140 669 Planarity : 0.003 0.036 767 Dihedral : 4.310 29.964 584 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.83 % Allowed : 28.04 % Favored : 69.13 % 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: 1.91 (0.39), residues: 536 helix: 1.79 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.44 (0.66), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1455 HIS 0.002 0.001 HIS A1257 PHE 0.005 0.001 PHE A1457 TYR 0.009 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 31 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 18 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (mt-10) outliers start: 13 outliers final: 8 residues processed: 31 average time/residue: 1.1127 time to fit residues: 36.4545 Evaluate side-chains 24 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1113 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 1492 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2933 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= 0.160 Angle : 0.550 11.128 6005 Z= 0.269 Chirality : 0.035 0.140 669 Planarity : 0.003 0.036 767 Dihedral : 4.257 28.104 584 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.04 % Allowed : 26.74 % Favored : 70.22 % 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 (0.39), residues: 536 helix: 1.87 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.52 (0.67), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1455 HIS 0.002 0.001 HIS A1111 PHE 0.005 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 30 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 16 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7837 (mt-10) outliers start: 14 outliers final: 8 residues processed: 30 average time/residue: 1.0371 time to fit residues: 32.9487 Evaluate side-chains 24 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1113 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 1492 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4435 Z= 0.146 Angle : 0.544 10.918 6005 Z= 0.265 Chirality : 0.035 0.140 669 Planarity : 0.003 0.036 767 Dihedral : 4.176 28.531 584 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.61 % Allowed : 27.17 % Favored : 70.22 % 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: 2.14 (0.39), residues: 536 helix: 1.99 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.49 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1455 HIS 0.002 0.001 HIS A1111 PHE 0.005 0.001 PHE A1457 TYR 0.009 0.001 TYR A1282 ARG 0.001 0.000 ARG A 942 *********************** 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 30 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 18 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 944 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 1225 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: A 1388 HIS cc_start: 0.3597 (OUTLIER) cc_final: 0.3251 (t-170) outliers start: 12 outliers final: 7 residues processed: 30 average time/residue: 1.2805 time to fit residues: 40.2945 Evaluate side-chains 27 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 17 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1225 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1775 > 50: distance: 26 - 30: 14.231 distance: 30 - 31: 25.464 distance: 31 - 32: 21.336 distance: 31 - 34: 27.753 distance: 32 - 33: 28.873 distance: 32 - 38: 14.887 distance: 34 - 35: 25.289 distance: 35 - 36: 26.595 distance: 35 - 37: 7.934 distance: 38 - 39: 17.876 distance: 39 - 40: 13.129 distance: 39 - 42: 14.965 distance: 40 - 41: 32.239 distance: 40 - 46: 19.539 distance: 42 - 43: 30.839 distance: 43 - 44: 15.275 distance: 43 - 45: 19.925 distance: 46 - 47: 8.280 distance: 47 - 48: 6.972 distance: 47 - 50: 19.537 distance: 48 - 49: 15.430 distance: 48 - 53: 20.958 distance: 50 - 51: 20.351 distance: 50 - 52: 15.209 distance: 53 - 54: 28.105 distance: 53 - 59: 30.529 distance: 54 - 55: 12.522 distance: 54 - 57: 34.803 distance: 55 - 56: 20.414 distance: 55 - 60: 27.141 distance: 57 - 58: 21.252 distance: 58 - 59: 21.570 distance: 60 - 61: 12.783 distance: 61 - 62: 21.649 distance: 61 - 64: 16.268 distance: 62 - 63: 13.035 distance: 62 - 69: 5.920 distance: 64 - 65: 10.289 distance: 65 - 66: 21.343 distance: 66 - 67: 14.646 distance: 66 - 68: 18.108 distance: 69 - 70: 10.221 distance: 70 - 71: 15.999 distance: 70 - 73: 8.604 distance: 71 - 72: 27.926 distance: 71 - 78: 10.531 distance: 72 - 108: 33.861 distance: 73 - 74: 10.846 distance: 74 - 75: 12.981 distance: 75 - 76: 8.800 distance: 75 - 77: 5.449 distance: 78 - 79: 16.057 distance: 79 - 80: 6.854 distance: 79 - 82: 30.268 distance: 80 - 81: 19.367 distance: 80 - 90: 11.604 distance: 81 - 113: 23.173 distance: 82 - 83: 5.424 distance: 83 - 84: 24.881 distance: 83 - 85: 8.222 distance: 84 - 86: 12.567 distance: 85 - 87: 13.251 distance: 86 - 88: 10.269 distance: 87 - 88: 22.589 distance: 88 - 89: 25.811 distance: 90 - 91: 3.916 distance: 91 - 92: 19.284 distance: 91 - 94: 19.775 distance: 92 - 93: 11.734 distance: 92 - 99: 4.483 distance: 93 - 119: 24.177 distance: 94 - 95: 8.202 distance: 95 - 96: 15.766 distance: 96 - 97: 18.245 distance: 96 - 98: 10.269 distance: 99 - 100: 10.860 distance: 100 - 101: 7.501 distance: 100 - 103: 3.852 distance: 101 - 102: 6.537 distance: 101 - 108: 4.800 distance: 102 - 128: 30.042 distance: 103 - 104: 8.796 distance: 104 - 105: 19.892 distance: 105 - 106: 10.469 distance: 105 - 107: 8.482 distance: 108 - 109: 22.651 distance: 109 - 110: 14.405 distance: 109 - 112: 14.830 distance: 110 - 111: 15.080 distance: 110 - 113: 26.855 distance: 111 - 136: 36.401