Starting phenix.real_space_refine on Thu Sep 26 17:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/09_2024/7si6_25138.cif" } resolution = 3.32 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 49 5.16 5 C 4239 2.51 5 N 1109 2.21 5 O 1202 1.98 5 F 4 1.80 5 H 6910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 13509 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 34, 'TRANS': 838} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.98, per 1000 atoms: 0.52 Number of scatterers: 13515 At special positions: 0 Unit cell: (90.95, 93.5, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1202 8.00 N 1109 7.00 C 4239 6.00 H 6910 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 499 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.611A pdb=" N VAL A 576 " --> pdb=" O CYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 623 removed outlier: 3.505A pdb=" N ILE A 615 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 657 Processing helix chain 'A' and resid 658 through 671 Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 707 through 721 removed outlier: 4.410A pdb=" N PHE A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 Processing helix chain 'A' and resid 762 through 783 Processing helix chain 'A' and resid 787 through 796 removed outlier: 3.562A pdb=" N GLN A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 891 through 907 Processing helix chain 'A' and resid 912 through 943 removed outlier: 3.528A pdb=" N TYR A 920 " --> pdb=" O LYS A 916 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 959 through 980 removed outlier: 3.521A pdb=" N CYS A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 985 removed outlier: 3.691A pdb=" N LEU A 984 " --> pdb=" O PRO A 981 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 985 " --> pdb=" O CYS A 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 981 through 985' Processing helix chain 'A' and resid 986 through 1003 removed outlier: 3.555A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1049 through 1062 Processing helix chain 'A' and resid 1066 through 1080 Processing helix chain 'A' and resid 1105 through 1112 removed outlier: 3.543A pdb=" N VAL A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1164 Processing helix chain 'A' and resid 1168 through 1182 Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1250 through 1264 Processing helix chain 'A' and resid 1276 through 1284 removed outlier: 4.600A pdb=" N ALA A1280 " --> pdb=" O ASN A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1301 Processing helix chain 'A' and resid 1310 through 1346 removed outlier: 4.182A pdb=" N VAL A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASN A1338 " --> pdb=" O ALA A1334 " (cutoff:3.500A) Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1357 through 1379 removed outlier: 4.035A pdb=" N GLY A1361 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A1362 " --> pdb=" O PRO A1358 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1365 " --> pdb=" O GLY A1361 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1379 " --> pdb=" O SER A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'A' and resid 1386 through 1394 Processing sheet with id=AA1, first strand: chain 'A' and resid 513 through 518 Processing sheet with id=AA2, first strand: chain 'A' and resid 589 through 594 Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 818 removed outlier: 4.241A pdb=" N ALA A 801 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 827 " --> pdb=" O VAL A 803 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP A 839 " --> pdb=" O THR A 885 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 840 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 861 through 863 Processing sheet with id=AA5, first strand: chain 'A' and resid 1004 through 1006 removed outlier: 6.178A pdb=" N GLY A1287 " --> pdb=" O ILE A1303 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU A1305 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA A1289 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A1268 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE A1288 " --> pdb=" O VAL A1268 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET A1270 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE A1290 " --> pdb=" O MET A1270 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY A1272 " --> pdb=" O ILE A1290 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A1020 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A1271 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET A1022 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A1222 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N PHE A1246 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A1224 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1245 " --> pdb=" O HIS A1409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1035 through 1041 removed outlier: 6.832A pdb=" N ALA A1199 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A1039 " --> pdb=" O MET A1197 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET A1197 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU A1041 " --> pdb=" O CYS A1195 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N CYS A1195 " --> pdb=" O LEU A1041 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A1190 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1170 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: 5.26 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6895 1.04 - 1.23: 78 1.23 - 1.43: 2504 1.43 - 1.62: 4050 1.62 - 1.82: 87 Bond restraints: 13614 Sorted by residual: bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CA VAL A 686 " pdb=" CB VAL A 686 " ideal model delta sigma weight residual 1.546 1.538 0.008 8.80e-03 1.29e+04 9.14e-01 ... (remaining 13609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 24804 14.24 - 28.48: 4 28.48 - 42.71: 0 42.71 - 56.95: 0 56.95 - 71.19: 2 Bond angle restraints: 24810 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.92 -70.29 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 90.05 20.16 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.69 89.99 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.59 89.92 19.67 3.00e+00 1.11e-01 4.30e+01 ... (remaining 24805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5729 17.01 - 34.02: 438 34.02 - 51.03: 109 51.03 - 68.04: 34 68.04 - 85.05: 12 Dihedral angle restraints: 6322 sinusoidal: 3524 harmonic: 2798 Sorted by residual: dihedral pdb=" CB CYS A 496 " pdb=" SG CYS A 496 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual 93.00 119.14 -26.14 1 1.00e+01 1.00e-02 9.82e+00 dihedral pdb=" CB MET A 993 " pdb=" CG MET A 993 " pdb=" SD MET A 993 " pdb=" CE MET A 993 " ideal model delta sinusoidal sigma weight residual 60.00 118.69 -58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A1234 " pdb=" CG LYS A1234 " pdb=" CD LYS A1234 " pdb=" CE LYS A1234 " ideal model delta sinusoidal sigma weight residual 60.00 112.40 -52.40 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 6319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 716 0.027 - 0.055: 201 0.055 - 0.082: 104 0.082 - 0.109: 65 0.109 - 0.136: 31 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CA VAL A1094 " pdb=" N VAL A1094 " pdb=" C VAL A1094 " pdb=" CB VAL A1094 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A1152 " pdb=" N VAL A1152 " pdb=" C VAL A1152 " pdb=" CB VAL A1152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL A 686 " pdb=" N VAL A 686 " pdb=" C VAL A 686 " pdb=" CB VAL A 686 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1114 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 951 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 952 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1342 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A1343 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1343 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1343 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1321 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C LYS A1321 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS A1321 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A1322 " -0.007 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1009 2.23 - 2.82: 30785 2.82 - 3.41: 35400 3.41 - 4.01: 47283 4.01 - 4.60: 72849 Nonbonded interactions: 187326 Sorted by model distance: nonbonded pdb=" OD1 ASP A 839 " pdb=" H ALA A 871 " model vdw 1.637 2.450 nonbonded pdb=" O LEU A1012 " pdb=" HG SER A1320 " model vdw 1.650 2.450 nonbonded pdb=" HZ2 LYS A1254 " pdb=" OD1 ASP A1277 " model vdw 1.699 2.450 nonbonded pdb=" OD1 ASN A 875 " pdb=" H ALA A 876 " model vdw 1.736 2.450 nonbonded pdb=" O VAL A1355 " pdb="HE22 GLN A1357 " model vdw 1.767 2.450 ... (remaining 187321 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 6704 Z= 0.201 Angle : 1.218 71.188 9081 Z= 0.452 Chirality : 0.042 0.136 1117 Planarity : 0.003 0.039 1130 Dihedral : 13.578 85.051 2459 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 2.88 (0.29), residues: 861 helix: 2.71 (0.24), residues: 464 sheet: 1.07 (0.46), residues: 128 loop : 1.01 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 721 PHE 0.011 0.001 PHE A 696 TYR 0.006 0.001 TYR A 710 ARG 0.007 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 GLU cc_start: 0.6837 (mp0) cc_final: 0.6605 (mp0) REVERT: A 815 GLU cc_start: 0.6773 (tt0) cc_final: 0.6510 (tt0) REVERT: A 1217 SER cc_start: 0.8208 (m) cc_final: 0.7973 (m) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3495 time to fit residues: 67.8087 Evaluate side-chains 108 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6704 Z= 0.189 Angle : 0.845 32.522 9081 Z= 0.344 Chirality : 0.043 0.139 1117 Planarity : 0.003 0.033 1130 Dihedral : 3.423 16.655 913 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.03 % 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: 2.89 (0.29), residues: 861 helix: 2.71 (0.23), residues: 473 sheet: 0.93 (0.45), residues: 128 loop : 1.02 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.002 0.001 HIS A1409 PHE 0.019 0.001 PHE A 944 TYR 0.010 0.001 TYR A1337 ARG 0.005 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 874 ILE cc_start: 0.8337 (mm) cc_final: 0.8022 (mm) REVERT: A 1217 SER cc_start: 0.8211 (m) cc_final: 0.7987 (m) REVERT: A 1248 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8118 (mp0) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.3389 time to fit residues: 50.4981 Evaluate side-chains 101 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 79 optimal weight: 0.0000 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 overall best weight: 2.5590 ------------------------------------------------------------------------------- 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: 0.7660 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6704 Z= 0.198 Angle : 0.839 31.919 9081 Z= 0.339 Chirality : 0.043 0.146 1117 Planarity : 0.003 0.037 1130 Dihedral : 3.534 17.334 913 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.69 % Allowed : 5.94 % Favored : 93.37 % 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: 2.66 (0.28), residues: 861 helix: 2.56 (0.23), residues: 475 sheet: 1.06 (0.44), residues: 138 loop : 0.67 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.009 0.001 PHE A 768 TYR 0.005 0.001 TYR A 712 ARG 0.004 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1217 SER cc_start: 0.8194 (m) cc_final: 0.7955 (m) REVERT: A 1309 ASP cc_start: 0.6856 (m-30) cc_final: 0.6583 (m-30) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.3440 time to fit residues: 53.2123 Evaluate side-chains 108 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6704 Z= 0.205 Angle : 0.839 32.274 9081 Z= 0.339 Chirality : 0.043 0.154 1117 Planarity : 0.003 0.039 1130 Dihedral : 3.557 17.579 913 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.97 % Allowed : 7.60 % Favored : 91.44 % 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: 2.54 (0.28), residues: 861 helix: 2.49 (0.23), residues: 475 sheet: 0.96 (0.43), residues: 138 loop : 0.59 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.008 0.001 PHE A 770 TYR 0.007 0.001 TYR A 712 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8253 (tpp) cc_final: 0.7774 (tpp) REVERT: A 1217 SER cc_start: 0.8167 (m) cc_final: 0.7931 (m) REVERT: A 1270 MET cc_start: 0.7920 (tpt) cc_final: 0.5461 (tpt) outliers start: 7 outliers final: 5 residues processed: 110 average time/residue: 0.3614 time to fit residues: 54.8209 Evaluate side-chains 110 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6704 Z= 0.195 Angle : 0.836 32.359 9081 Z= 0.337 Chirality : 0.043 0.143 1117 Planarity : 0.003 0.056 1130 Dihedral : 3.586 17.722 913 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.83 % Allowed : 8.15 % Favored : 91.02 % 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: 2.53 (0.29), residues: 861 helix: 2.52 (0.23), residues: 474 sheet: 0.90 (0.44), residues: 138 loop : 0.55 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.009 0.001 PHE A 770 TYR 0.007 0.001 TYR A 712 ARG 0.004 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8235 (tpp) cc_final: 0.7769 (tpp) REVERT: A 874 ILE cc_start: 0.8417 (mm) cc_final: 0.8108 (mm) REVERT: A 1217 SER cc_start: 0.8140 (m) cc_final: 0.7913 (m) REVERT: A 1270 MET cc_start: 0.7879 (tpt) cc_final: 0.5474 (tpt) REVERT: A 1390 TYR cc_start: 0.7473 (m-10) cc_final: 0.7130 (m-10) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.3396 time to fit residues: 54.6112 Evaluate side-chains 112 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6704 Z= 0.250 Angle : 0.852 33.587 9081 Z= 0.349 Chirality : 0.044 0.153 1117 Planarity : 0.004 0.046 1130 Dihedral : 3.707 18.576 913 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.38 % Allowed : 8.98 % Favored : 89.64 % 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: 2.40 (0.29), residues: 861 helix: 2.39 (0.23), residues: 474 sheet: 0.95 (0.43), residues: 143 loop : 0.46 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.009 0.002 PHE A1333 TYR 0.007 0.001 TYR A 712 ARG 0.005 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8220 (tpp) cc_final: 0.7833 (tpp) REVERT: A 874 ILE cc_start: 0.8471 (mm) cc_final: 0.8164 (mm) REVERT: A 1217 SER cc_start: 0.8132 (m) cc_final: 0.7899 (m) REVERT: A 1270 MET cc_start: 0.7851 (tpt) cc_final: 0.5489 (tpt) REVERT: A 1309 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: A 1390 TYR cc_start: 0.7603 (m-80) cc_final: 0.7220 (m-10) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.3474 time to fit residues: 56.8855 Evaluate side-chains 119 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1309 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6704 Z= 0.151 Angle : 0.833 31.403 9081 Z= 0.334 Chirality : 0.043 0.143 1117 Planarity : 0.003 0.043 1130 Dihedral : 3.556 17.571 913 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.69 % Allowed : 10.77 % Favored : 88.54 % 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: 2.59 (0.29), residues: 861 helix: 2.57 (0.24), residues: 474 sheet: 0.98 (0.43), residues: 143 loop : 0.54 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 936 HIS 0.002 0.000 HIS A 779 PHE 0.009 0.001 PHE A 770 TYR 0.007 0.001 TYR A 712 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8201 (tpp) cc_final: 0.7825 (tpp) REVERT: A 874 ILE cc_start: 0.8451 (mm) cc_final: 0.8120 (mm) REVERT: A 1217 SER cc_start: 0.8107 (m) cc_final: 0.7871 (m) REVERT: A 1270 MET cc_start: 0.7835 (tpt) cc_final: 0.5511 (tpt) REVERT: A 1299 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 1309 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6699 (m-30) outliers start: 5 outliers final: 4 residues processed: 109 average time/residue: 0.3518 time to fit residues: 53.8670 Evaluate side-chains 110 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1309 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.0570 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6704 Z= 0.148 Angle : 0.828 31.425 9081 Z= 0.330 Chirality : 0.043 0.150 1117 Planarity : 0.003 0.037 1130 Dihedral : 3.474 17.245 913 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.55 % Allowed : 10.50 % Favored : 88.95 % 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: 2.72 (0.29), residues: 861 helix: 2.70 (0.24), residues: 474 sheet: 1.03 (0.44), residues: 143 loop : 0.54 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 936 HIS 0.002 0.001 HIS A 877 PHE 0.010 0.001 PHE A 696 TYR 0.006 0.001 TYR A 712 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 MET cc_start: 0.7429 (mmm) cc_final: 0.7199 (tpp) REVERT: A 859 MET cc_start: 0.8175 (tpp) cc_final: 0.7806 (tpp) REVERT: A 874 ILE cc_start: 0.8417 (mm) cc_final: 0.8051 (mm) REVERT: A 1022 MET cc_start: 0.8323 (mtm) cc_final: 0.7959 (mtm) REVERT: A 1217 SER cc_start: 0.8116 (m) cc_final: 0.7884 (m) REVERT: A 1270 MET cc_start: 0.7849 (tpt) cc_final: 0.5570 (tpt) REVERT: A 1299 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6598 (mm-30) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.3338 time to fit residues: 52.3477 Evaluate side-chains 114 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6704 Z= 0.168 Angle : 0.835 31.908 9081 Z= 0.334 Chirality : 0.043 0.143 1117 Planarity : 0.004 0.064 1130 Dihedral : 3.497 17.058 913 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.83 % Allowed : 10.36 % Favored : 88.81 % 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: 2.66 (0.29), residues: 861 helix: 2.64 (0.24), residues: 474 sheet: 1.01 (0.44), residues: 143 loop : 0.53 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 936 HIS 0.003 0.000 HIS A 779 PHE 0.008 0.001 PHE A 770 TYR 0.006 0.001 TYR A 712 ARG 0.005 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8168 (tpp) cc_final: 0.7804 (tpp) REVERT: A 874 ILE cc_start: 0.8391 (mm) cc_final: 0.8015 (mm) REVERT: A 1217 SER cc_start: 0.8123 (m) cc_final: 0.7896 (m) REVERT: A 1265 ASN cc_start: 0.7602 (t0) cc_final: 0.7223 (t0) REVERT: A 1270 MET cc_start: 0.7841 (tpt) cc_final: 0.5546 (tpt) REVERT: A 1299 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6643 (mm-30) REVERT: A 1309 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: A 1390 TYR cc_start: 0.7766 (m-80) cc_final: 0.7405 (m-10) outliers start: 6 outliers final: 5 residues processed: 115 average time/residue: 0.3720 time to fit residues: 59.2201 Evaluate side-chains 116 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6704 Z= 0.190 Angle : 0.841 32.333 9081 Z= 0.339 Chirality : 0.043 0.147 1117 Planarity : 0.004 0.064 1130 Dihedral : 3.550 17.676 913 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.69 % Allowed : 10.64 % Favored : 88.67 % 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: 2.56 (0.29), residues: 861 helix: 2.55 (0.24), residues: 474 sheet: 0.98 (0.44), residues: 143 loop : 0.50 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 PHE 0.009 0.001 PHE A 696 TYR 0.007 0.001 TYR A 712 ARG 0.007 0.000 ARG A 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8160 (tpp) cc_final: 0.7797 (tpp) REVERT: A 874 ILE cc_start: 0.8420 (mm) cc_final: 0.8040 (mm) REVERT: A 1217 SER cc_start: 0.8121 (m) cc_final: 0.7892 (m) REVERT: A 1265 ASN cc_start: 0.7598 (t0) cc_final: 0.7210 (t0) REVERT: A 1270 MET cc_start: 0.7844 (tpt) cc_final: 0.5590 (tpt) REVERT: A 1299 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6801 (mm-30) REVERT: A 1309 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: A 1390 TYR cc_start: 0.7800 (m-80) cc_final: 0.7446 (m-10) outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 0.3331 time to fit residues: 53.3799 Evaluate side-chains 116 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.203058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128304 restraints weight = 21532.806| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.56 r_work: 0.3150 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6704 Z= 0.154 Angle : 0.835 31.455 9081 Z= 0.334 Chirality : 0.043 0.143 1117 Planarity : 0.004 0.061 1130 Dihedral : 3.491 17.084 913 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.55 % Allowed : 11.19 % Favored : 88.26 % 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: 2.65 (0.29), residues: 861 helix: 2.61 (0.24), residues: 474 sheet: 1.01 (0.44), residues: 143 loop : 0.57 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 936 HIS 0.002 0.000 HIS A 779 PHE 0.009 0.001 PHE A 696 TYR 0.006 0.001 TYR A 712 ARG 0.005 0.000 ARG A 824 =============================================================================== Job complete usr+sys time: 3346.01 seconds wall clock time: 58 minutes 42.14 seconds (3522.14 seconds total)