Starting phenix.real_space_refine on Wed Mar 4 12:44:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_25138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_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/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_25138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_25138.map" model { file = "/net/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_25138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7si6_25138/03_2026/7si6_25138.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'ARG: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: 2.35, per 1000 atoms: 0.17 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: 1.14 Conformation dependent library (CDL) restraints added in 421.2 milliseconds 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: 0.41 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: 2.85 Time building geometry restraints manager: 1.64 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: 0.120 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: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- 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 6705 Z= 0.155 Angle : 1.218 71.188 9083 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG A 824 TYR 0.006 0.001 TYR A 710 PHE 0.011 0.001 PHE A 696 TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6704) covalent geometry : angle 1.21831 ( 9081) SS BOND : bond 0.00166 ( 1) SS BOND : angle 1.50394 ( 2) hydrogen bonds : bond 0.12897 ( 402) hydrogen bonds : angle 5.31326 ( 1170) *********************** 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 to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.351 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: 0.8209 (m) cc_final: 0.7973 (m) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1536 time to fit residues: 29.7648 Evaluate side-chains 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.206696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140639 restraints weight = 21633.303| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.91 r_work: 0.3235 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6705 Z= 0.143 Angle : 0.853 32.968 9083 Z= 0.349 Chirality : 0.043 0.139 1117 Planarity : 0.003 0.034 1130 Dihedral : 3.490 17.101 913 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.69 % Allowed : 4.14 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.28), residues: 861 helix: 2.63 (0.23), residues: 473 sheet: 0.92 (0.45), residues: 128 loop : 0.99 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1157 TYR 0.010 0.001 TYR A1337 PHE 0.014 0.001 PHE A 944 TRP 0.009 0.001 TRP A 936 HIS 0.002 0.001 HIS A1409 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6704) covalent geometry : angle 0.85134 ( 9081) SS BOND : bond 0.00401 ( 1) SS BOND : angle 3.62069 ( 2) hydrogen bonds : bond 0.04294 ( 402) hydrogen bonds : angle 4.37670 ( 1170) *********************** 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 107 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.1533 time to fit residues: 22.8207 Evaluate side-chains 100 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 948 ILE Chi-restraints excluded: chain A residue 1295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 58 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.205042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130185 restraints weight = 21652.672| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.58 r_work: 0.3151 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6705 Z= 0.170 Angle : 0.854 33.322 9083 Z= 0.350 Chirality : 0.044 0.146 1117 Planarity : 0.003 0.040 1130 Dihedral : 3.630 17.806 913 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.97 % Allowed : 6.49 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.28), residues: 861 helix: 2.40 (0.23), residues: 475 sheet: 1.01 (0.44), residues: 138 loop : 0.57 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 824 TYR 0.006 0.001 TYR A 712 PHE 0.010 0.002 PHE A 768 TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6704) covalent geometry : angle 0.85223 ( 9081) SS BOND : bond 0.00359 ( 1) SS BOND : angle 3.87439 ( 2) hydrogen bonds : bond 0.04358 ( 402) hydrogen bonds : angle 4.29628 ( 1170) *********************** 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 to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 GLU cc_start: 0.8322 (tt0) cc_final: 0.8018 (tp30) REVERT: A 1270 MET cc_start: 0.8403 (tpt) cc_final: 0.6087 (tpt) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.1650 time to fit residues: 24.9272 Evaluate side-chains 106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 948 ILE Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.203834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128749 restraints weight = 21561.151| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.56 r_work: 0.3131 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6705 Z= 0.161 Angle : 0.855 32.895 9083 Z= 0.352 Chirality : 0.044 0.160 1117 Planarity : 0.004 0.042 1130 Dihedral : 3.692 18.393 913 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.66 % Allowed : 7.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.28), residues: 861 helix: 2.31 (0.23), residues: 474 sheet: 0.90 (0.44), residues: 138 loop : 0.46 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.007 0.001 TYR A 712 PHE 0.023 0.002 PHE A 696 TRP 0.008 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6704) covalent geometry : angle 0.85325 ( 9081) SS BOND : bond 0.00413 ( 1) SS BOND : angle 3.86181 ( 2) hydrogen bonds : bond 0.04146 ( 402) hydrogen bonds : angle 4.21945 ( 1170) *********************** 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 117 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 GLU cc_start: 0.8309 (tt0) cc_final: 0.8011 (tp30) REVERT: A 859 MET cc_start: 0.8580 (tpp) cc_final: 0.8162 (tpp) REVERT: A 1270 MET cc_start: 0.8376 (tpt) cc_final: 0.6107 (tpt) REVERT: A 1309 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7164 (m-30) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.1796 time to fit residues: 27.3023 Evaluate side-chains 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 1202 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 0.4980 chunk 60 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.201288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126132 restraints weight = 21778.305| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6705 Z= 0.227 Angle : 0.885 36.810 9083 Z= 0.375 Chirality : 0.045 0.162 1117 Planarity : 0.004 0.062 1130 Dihedral : 3.998 19.418 913 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.10 % Allowed : 9.39 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 861 helix: 1.99 (0.24), residues: 472 sheet: 0.96 (0.44), residues: 142 loop : 0.45 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 824 TYR 0.009 0.001 TYR A 712 PHE 0.015 0.002 PHE A 760 TRP 0.007 0.001 TRP A 936 HIS 0.004 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 6704) covalent geometry : angle 0.88302 ( 9081) SS BOND : bond 0.00441 ( 1) SS BOND : angle 3.98676 ( 2) hydrogen bonds : bond 0.04636 ( 402) hydrogen bonds : angle 4.36212 ( 1170) *********************** 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 120 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 GLU cc_start: 0.8302 (tt0) cc_final: 0.8051 (tp30) REVERT: A 859 MET cc_start: 0.8533 (tpp) cc_final: 0.8226 (tpp) REVERT: A 1265 ASN cc_start: 0.7924 (t0) cc_final: 0.7605 (t0) REVERT: A 1270 MET cc_start: 0.8383 (tpt) cc_final: 0.6276 (tpt) REVERT: A 1390 TYR cc_start: 0.7599 (m-80) cc_final: 0.7229 (m-10) outliers start: 8 outliers final: 7 residues processed: 116 average time/residue: 0.1732 time to fit residues: 27.6577 Evaluate side-chains 116 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 948 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.200350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131774 restraints weight = 21690.722| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.84 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6705 Z= 0.186 Angle : 0.865 35.745 9083 Z= 0.359 Chirality : 0.045 0.167 1117 Planarity : 0.004 0.062 1130 Dihedral : 3.940 19.120 913 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.52 % Allowed : 10.91 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.29), residues: 861 helix: 2.00 (0.24), residues: 474 sheet: 0.86 (0.44), residues: 142 loop : 0.44 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.011 0.001 TYR A 712 PHE 0.014 0.002 PHE A 657 TRP 0.008 0.001 TRP A 936 HIS 0.004 0.001 HIS A 886 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6704) covalent geometry : angle 0.86322 ( 9081) SS BOND : bond 0.00459 ( 1) SS BOND : angle 3.84796 ( 2) hydrogen bonds : bond 0.04243 ( 402) hydrogen bonds : angle 4.24456 ( 1170) *********************** 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 122 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.7954 (mtp) cc_final: 0.7745 (mtp) REVERT: A 859 MET cc_start: 0.8493 (tpp) cc_final: 0.8200 (tpp) REVERT: A 1265 ASN cc_start: 0.7931 (t0) cc_final: 0.7569 (t0) REVERT: A 1270 MET cc_start: 0.8370 (tpt) cc_final: 0.6311 (tpt) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.1727 time to fit residues: 27.3635 Evaluate side-chains 117 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 689 LEU 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 1202 ASP Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1295 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 50.0000 chunk 74 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.202145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133751 restraints weight = 21610.149| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.92 r_work: 0.3138 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6705 Z= 0.114 Angle : 0.838 31.963 9083 Z= 0.338 Chirality : 0.043 0.145 1117 Planarity : 0.003 0.042 1130 Dihedral : 3.740 18.474 913 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.69 % Allowed : 11.60 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.29), residues: 861 helix: 2.27 (0.24), residues: 475 sheet: 0.86 (0.44), residues: 142 loop : 0.56 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.008 0.001 TYR A 712 PHE 0.009 0.001 PHE A 770 TRP 0.011 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6704) covalent geometry : angle 0.83657 ( 9081) SS BOND : bond 0.00471 ( 1) SS BOND : angle 3.73555 ( 2) hydrogen bonds : bond 0.03674 ( 402) hydrogen bonds : angle 4.04980 ( 1170) *********************** 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 114 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8491 (tpp) cc_final: 0.8205 (tpp) REVERT: A 1265 ASN cc_start: 0.7936 (t0) cc_final: 0.7539 (t0) outliers start: 5 outliers final: 4 residues processed: 111 average time/residue: 0.1803 time to fit residues: 26.9771 Evaluate side-chains 113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.199563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124214 restraints weight = 21566.257| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.51 r_work: 0.3084 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6705 Z= 0.199 Angle : 0.866 34.665 9083 Z= 0.360 Chirality : 0.045 0.169 1117 Planarity : 0.004 0.044 1130 Dihedral : 3.902 19.457 913 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.80 % Allowed : 11.05 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.29), residues: 861 helix: 2.11 (0.24), residues: 472 sheet: 0.76 (0.44), residues: 142 loop : 0.44 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 824 TYR 0.009 0.001 TYR A 712 PHE 0.011 0.002 PHE A1023 TRP 0.008 0.001 TRP A 936 HIS 0.004 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 6704) covalent geometry : angle 0.86446 ( 9081) SS BOND : bond 0.00501 ( 1) SS BOND : angle 3.83837 ( 2) hydrogen bonds : bond 0.04250 ( 402) hydrogen bonds : angle 4.18111 ( 1170) *********************** 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 121 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8542 (tpp) cc_final: 0.8249 (tpp) REVERT: A 1309 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (t70) REVERT: A 1390 TYR cc_start: 0.7780 (m-80) cc_final: 0.7445 (m-10) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.1914 time to fit residues: 29.7767 Evaluate side-chains 118 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 992 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 50.0000 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.201836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125812 restraints weight = 21727.663| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.57 r_work: 0.3112 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6705 Z= 0.113 Angle : 0.840 31.782 9083 Z= 0.339 Chirality : 0.043 0.149 1117 Planarity : 0.003 0.039 1130 Dihedral : 3.745 18.439 913 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.83 % Allowed : 12.02 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.29), residues: 861 helix: 2.27 (0.24), residues: 475 sheet: 0.80 (0.44), residues: 142 loop : 0.50 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.006 0.001 TYR A 712 PHE 0.009 0.001 PHE A 770 TRP 0.011 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6704) covalent geometry : angle 0.83799 ( 9081) SS BOND : bond 0.00501 ( 1) SS BOND : angle 3.68981 ( 2) hydrogen bonds : bond 0.03675 ( 402) hydrogen bonds : angle 4.00744 ( 1170) *********************** 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 116 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7152 (tp40) REVERT: A 820 GLU cc_start: 0.8335 (tt0) cc_final: 0.8093 (mm-30) REVERT: A 859 MET cc_start: 0.8541 (tpp) cc_final: 0.8238 (tpp) REVERT: A 1265 ASN cc_start: 0.7866 (t0) cc_final: 0.7460 (t0) REVERT: A 1270 MET cc_start: 0.8342 (tpt) cc_final: 0.6306 (tpt) REVERT: A 1309 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7376 (t70) REVERT: A 1390 TYR cc_start: 0.7780 (m-80) cc_final: 0.7445 (m-10) outliers start: 6 outliers final: 5 residues processed: 112 average time/residue: 0.2010 time to fit residues: 30.1186 Evaluate side-chains 114 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1263 SER 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 27 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.200992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125250 restraints weight = 21693.076| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.54 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6705 Z= 0.145 Angle : 0.850 33.173 9083 Z= 0.346 Chirality : 0.043 0.153 1117 Planarity : 0.004 0.070 1130 Dihedral : 3.772 18.693 913 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 11.74 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.29), residues: 861 helix: 2.24 (0.24), residues: 475 sheet: 0.79 (0.44), residues: 142 loop : 0.46 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 824 TYR 0.007 0.001 TYR A 712 PHE 0.009 0.001 PHE A 760 TRP 0.009 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6704) covalent geometry : angle 0.84823 ( 9081) SS BOND : bond 0.00507 ( 1) SS BOND : angle 3.74824 ( 2) hydrogen bonds : bond 0.03854 ( 402) hydrogen bonds : angle 4.03475 ( 1170) ********************** 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 to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7130 (mm110) REVERT: A 820 GLU cc_start: 0.8323 (tt0) cc_final: 0.7994 (mt-10) REVERT: A 859 MET cc_start: 0.8538 (tpp) cc_final: 0.8239 (tpp) REVERT: A 1270 MET cc_start: 0.8345 (tpt) cc_final: 0.6295 (tpt) REVERT: A 1309 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7520 (t70) REVERT: A 1390 TYR cc_start: 0.7825 (m-80) cc_final: 0.7506 (m-10) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.1920 time to fit residues: 29.2136 Evaluate side-chains 115 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 689 LEU 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 1309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.202053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.126921 restraints weight = 21587.483| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.53 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6705 Z= 0.116 Angle : 0.842 32.028 9083 Z= 0.340 Chirality : 0.043 0.144 1117 Planarity : 0.004 0.070 1130 Dihedral : 3.704 18.287 913 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.10 % Allowed : 11.88 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.29), residues: 861 helix: 2.32 (0.24), residues: 475 sheet: 0.78 (0.44), residues: 142 loop : 0.50 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 824 TYR 0.006 0.001 TYR A 712 PHE 0.009 0.001 PHE A 770 TRP 0.010 0.001 TRP A 936 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6704) covalent geometry : angle 0.84003 ( 9081) SS BOND : bond 0.00651 ( 1) SS BOND : angle 4.02117 ( 2) hydrogen bonds : bond 0.03617 ( 402) hydrogen bonds : angle 3.98256 ( 1170) =============================================================================== Job complete usr+sys time: 3946.10 seconds wall clock time: 67 minutes 27.35 seconds (4047.35 seconds total)