Starting phenix.real_space_refine on Wed Aug 5 09:18:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.cif Found real_map, /net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.map" model { file = "/net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11go_75680/08_2026/11go_75680.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 5463 2.51 5 N 1519 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8840 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8321 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 1045} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' MG': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.91, per 1000 atoms: 0.22 Number of scatterers: 8840 At special positions: 0 Unit cell: (93.09, 98.44, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 28 15.00 Mg 1 11.99 O 1790 8.00 N 1519 7.00 C 5463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 222.8 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 62.8% alpha, 5.3% beta 6 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 3.664A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1059 Processing helix chain 'A' and resid 1061 through 1070 Processing helix chain 'A' and resid 1079 through 1110 removed outlier: 3.515A pdb=" N ILE A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1118 Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1145 through 1163 Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 3.649A pdb=" N GLY A1197 " --> pdb=" O GLN A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 removed outlier: 3.602A pdb=" N GLY A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1229 Processing helix chain 'A' and resid 1229 through 1246 removed outlier: 3.744A pdb=" N THR A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1322 through 1334 Processing helix chain 'A' and resid 1340 through 1351 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1365 through 1369 Processing helix chain 'A' and resid 1370 through 1400 removed outlier: 3.504A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A1379 " --> pdb=" O LYS A1375 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A1383 " --> pdb=" O GLY A1379 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.717A pdb=" N VAL A1408 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1468 through 1470 No H-bonds generated for 'chain 'A' and resid 1468 through 1470' Processing helix chain 'A' and resid 1471 through 1475 Processing helix chain 'A' and resid 1476 through 1489 Processing helix chain 'A' and resid 1492 through 1506 Processing helix chain 'A' and resid 1511 through 1521 Processing helix chain 'A' and resid 1525 through 1541 Processing helix chain 'A' and resid 1559 through 1570 removed outlier: 3.681A pdb=" N THR A1570 " --> pdb=" O MET A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1583 Processing helix chain 'A' and resid 1595 through 1603 Processing helix chain 'A' and resid 1607 through 1627 removed outlier: 3.524A pdb=" N GLU A1618 " --> pdb=" O ASN A1614 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1648 removed outlier: 3.815A pdb=" N PHE A1647 " --> pdb=" O LEU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1674 removed outlier: 4.614A pdb=" N ASN A1668 " --> pdb=" O GLY A1664 " (cutoff:3.500A) Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1678 through 1708 removed outlier: 3.602A pdb=" N ILE A1682 " --> pdb=" O GLY A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1719 Processing helix chain 'A' and resid 1724 through 1744 Processing helix chain 'A' and resid 1776 through 1790 removed outlier: 3.520A pdb=" N ASN A1785 " --> pdb=" O ALA A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1803 Processing helix chain 'A' and resid 1803 through 1840 removed outlier: 3.738A pdb=" N VAL A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A1812 " --> pdb=" O TYR A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1862 Processing helix chain 'A' and resid 1915 through 1925 removed outlier: 3.512A pdb=" N MET A1920 " --> pdb=" O GLY A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1936 Processing helix chain 'A' and resid 1958 through 1972 Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.721A pdb=" N ASN A1990 " --> pdb=" O LYS A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1996 removed outlier: 3.509A pdb=" N LYS A1995 " --> pdb=" O ASP A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2009 removed outlier: 3.743A pdb=" N SER A2007 " --> pdb=" O ALA A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2048 removed outlier: 3.544A pdb=" N ASN A2035 " --> pdb=" O ARG A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2096 removed outlier: 3.541A pdb=" N ARG A2095 " --> pdb=" O GLU A2091 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A2096 " --> pdb=" O LEU A2092 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA2, first strand: chain 'A' and resid 1135 through 1138 Processing sheet with id=AA3, first strand: chain 'A' and resid 1249 through 1255 Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1302 removed outlier: 4.561A pdb=" N PHE A1301 " --> pdb=" O HIS A1411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AA6, first strand: chain 'A' and resid 1414 through 1416 Processing sheet with id=AA7, first strand: chain 'A' and resid 1445 through 1447 Processing sheet with id=AA8, first strand: chain 'A' and resid 1552 through 1554 removed outlier: 3.545A pdb=" N LEU A1944 " --> pdb=" O ASN A1951 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1587 through 1588 Processing sheet with id=AB1, first strand: chain 'A' and resid 1651 through 1653 Processing sheet with id=AB2, first strand: chain 'A' and resid 1745 through 1747 Processing sheet with id=AB3, first strand: chain 'A' and resid 1870 through 1871 Processing sheet with id=AB4, first strand: chain 'A' and resid 1881 through 1882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1891 through 1894 removed outlier: 6.889A pdb=" N VAL A1902 " --> pdb=" O LEU A1892 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2534 1.33 - 1.45: 1334 1.45 - 1.57: 5030 1.57 - 1.69: 53 1.69 - 1.80: 78 Bond restraints: 9029 Sorted by residual: bond pdb=" C3' DC C 19 " pdb=" C2' DC C 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.24e+00 bond pdb=" C3' DG C 18 " pdb=" O3' DG C 18 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" C3' DT C 23 " pdb=" C2' DT C 23 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.34e+00 bond pdb=" C3' DA C 12 " pdb=" O3' DA C 12 " ideal model delta sigma weight residual 1.435 1.406 0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" O4' DA C 12 " pdb=" C1' DA C 12 " ideal model delta sigma weight residual 1.420 1.395 0.025 1.10e-02 8.26e+03 5.05e+00 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 12171 2.11 - 4.22: 147 4.22 - 6.33: 17 6.33 - 8.44: 2 8.44 - 10.55: 2 Bond angle restraints: 12339 Sorted by residual: angle pdb=" C THR A1761 " pdb=" N GLY A1762 " pdb=" CA GLY A1762 " ideal model delta sigma weight residual 121.70 129.73 -8.03 1.80e+00 3.09e-01 1.99e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 23 " pdb=" C4 DT C 23 " pdb=" O4 DT C 23 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+01 angle pdb=" O4 DT C 21 " pdb=" C4 DT C 21 " pdb=" C5 DT C 21 " ideal model delta sigma weight residual 124.90 122.14 2.76 7.00e-01 2.04e+00 1.55e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 5282 34.37 - 68.73: 172 68.73 - 103.10: 10 103.10 - 137.46: 2 137.46 - 171.83: 4 Dihedral angle restraints: 5470 sinusoidal: 2311 harmonic: 3159 Sorted by residual: dihedral pdb=" C5' GTP A3301 " pdb=" O5' GTP A3301 " pdb=" PA GTP A3301 " pdb=" O3A GTP A3301 " ideal model delta sinusoidal sigma weight residual 69.27 -102.56 171.83 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A3302 " pdb=" C1' GTP A3302 " pdb=" N9 GTP A3302 " pdb=" O4' GTP A3302 " ideal model delta sinusoidal sigma weight residual 104.59 -24.86 129.45 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C8 GTP A3301 " pdb=" C1' GTP A3301 " pdb=" N9 GTP A3301 " pdb=" O4' GTP A3301 " ideal model delta sinusoidal sigma weight residual 104.59 -22.61 127.20 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1313 0.083 - 0.166: 106 0.166 - 0.249: 1 0.249 - 0.332: 0 0.332 - 0.415: 1 Chirality restraints: 1421 Sorted by residual: chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C3' DA C 17 " pdb=" C4' DA C 17 " pdb=" O3' DA C 17 " pdb=" C2' DA C 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASP A1469 " pdb=" N ASP A1469 " pdb=" C ASP A1469 " pdb=" CB ASP A1469 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1418 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1429 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1430 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1430 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1430 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2076 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A2077 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1668 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A1669 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A1669 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1669 " -0.018 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 53 2.54 - 3.13: 7144 3.13 - 3.72: 13973 3.72 - 4.31: 18323 4.31 - 4.90: 30921 Nonbonded interactions: 70414 Sorted by model distance: nonbonded pdb=" O3A GTP A3302 " pdb="MG MG A3303 " model vdw 1.948 2.170 nonbonded pdb=" O3G GTP A3302 " pdb="MG MG A3303 " model vdw 1.981 2.170 nonbonded pdb=" O2B GTP A3302 " pdb="MG MG A3303 " model vdw 2.027 2.170 nonbonded pdb=" OH TYR A1969 " pdb=" OD1 ASP A2048 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A2018 " pdb=" OD1 ASP A2020 " model vdw 2.203 3.040 ... (remaining 70409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.450 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.440 Find NCS groups from input model: 0.170 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.006 0.041 9029 Z= 0.309 Angle : 0.598 10.554 12339 Z= 0.358 Chirality : 0.045 0.415 1421 Planarity : 0.003 0.043 1523 Dihedral : 16.486 171.828 3430 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.41 (0.26), residues: 1088 helix: 2.76 (0.21), residues: 611 sheet: -0.12 (0.60), residues: 68 loop : 0.11 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1125 TYR 0.014 0.001 TYR A1388 PHE 0.010 0.001 PHE A1392 TRP 0.011 0.001 TRP A1159 HIS 0.002 0.001 HIS A1340 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.31 ( 9029) covalent geometry : angle 0.59848 / 0.36 (12339) hydrogen bonds : bond 0.17881 / 11.30 ( 507) hydrogen bonds : angle 5.86093 / 4.17 ( 1424) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.199 Fit side-chains REVERT: A 1480 MET cc_start: 0.9159 (tmm) cc_final: 0.8869 (tmm) REVERT: A 1567 MET cc_start: 0.9408 (tpt) cc_final: 0.9117 (tpt) REVERT: A 1696 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 1710 ASN cc_start: 0.9040 (m-40) cc_final: 0.8618 (p0) REVERT: A 1886 GLU cc_start: 0.9151 (tp30) cc_final: 0.8711 (tp30) REVERT: A 2075 MET cc_start: 0.8521 (mtt) cc_final: 0.8173 (mtm) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.6468 time to fit residues: 35.1254 Evaluate side-chains 48 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.048112 restraints weight = 26110.038| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.98 r_work: 0.2561 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9029 Z= 0.143 Angle : 0.554 7.465 12339 Z= 0.300 Chirality : 0.043 0.378 1421 Planarity : 0.004 0.044 1523 Dihedral : 16.481 178.022 1442 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.68 % Allowed : 7.45 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.48 (0.25), residues: 1088 helix: 2.77 (0.21), residues: 615 sheet: -0.10 (0.59), residues: 79 loop : 0.24 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2031 TYR 0.013 0.001 TYR A1388 PHE 0.009 0.001 PHE A1790 TRP 0.005 0.001 TRP A1578 HIS 0.001 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9029) covalent geometry : angle 0.55355 / 0.30 (12339) hydrogen bonds : bond 0.05571 / 3.70 ( 507) hydrogen bonds : angle 4.73993 / 3.40 ( 1424) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.286 Fit side-chains REVERT: A 1480 MET cc_start: 0.9147 (tmm) cc_final: 0.8806 (tmm) REVERT: A 1696 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 1710 ASN cc_start: 0.9026 (m-40) cc_final: 0.8616 (p0) REVERT: A 1869 MET cc_start: 0.6175 (mmp) cc_final: 0.5790 (mmt) REVERT: A 1886 GLU cc_start: 0.9144 (tp30) cc_final: 0.8692 (tp30) REVERT: A 1988 MET cc_start: 0.9173 (tpp) cc_final: 0.8695 (mmm) REVERT: A 2075 MET cc_start: 0.8509 (mtt) cc_final: 0.8183 (mtm) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.5945 time to fit residues: 32.2673 Evaluate side-chains 49 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1739 MET Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.046023 restraints weight = 26580.819| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.96 r_work: 0.2505 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9029 Z= 0.308 Angle : 0.644 7.488 12339 Z= 0.338 Chirality : 0.045 0.419 1421 Planarity : 0.004 0.047 1523 Dihedral : 16.476 176.697 1442 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.47 % Allowed : 8.58 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.19 (0.25), residues: 1088 helix: 2.63 (0.21), residues: 618 sheet: -0.23 (0.60), residues: 79 loop : -0.10 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1315 TYR 0.014 0.001 TYR A1388 PHE 0.009 0.001 PHE A1588 TRP 0.006 0.001 TRP A1159 HIS 0.003 0.001 HIS A1340 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.31 ( 9029) covalent geometry : angle 0.64369 / 0.34 (12339) hydrogen bonds : bond 0.05610 / 3.74 ( 507) hydrogen bonds : angle 4.67196 / 3.35 ( 1424) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.233 Fit side-chains REVERT: A 1480 MET cc_start: 0.9133 (tmm) cc_final: 0.8733 (tmm) REVERT: A 1533 MET cc_start: 0.9284 (tpt) cc_final: 0.8884 (tpt) REVERT: A 1567 MET cc_start: 0.9449 (tpt) cc_final: 0.9152 (tpt) REVERT: A 1710 ASN cc_start: 0.9028 (m-40) cc_final: 0.8648 (p0) REVERT: A 1869 MET cc_start: 0.6674 (mmp) cc_final: 0.6223 (mmt) REVERT: A 1886 GLU cc_start: 0.9153 (tp30) cc_final: 0.8747 (tm-30) REVERT: A 2075 MET cc_start: 0.8589 (mtt) cc_final: 0.8240 (mtm) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.4828 time to fit residues: 28.6329 Evaluate side-chains 51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.048764 restraints weight = 26373.321| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.00 r_work: 0.2575 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9029 Z= 0.119 Angle : 0.518 7.274 12339 Z= 0.277 Chirality : 0.041 0.377 1421 Planarity : 0.003 0.043 1523 Dihedral : 16.432 175.048 1442 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.79 % Allowed : 10.61 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1088 helix: 2.84 (0.21), residues: 616 sheet: -0.29 (0.60), residues: 79 loop : 0.09 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1315 TYR 0.008 0.001 TYR A1414 PHE 0.013 0.001 PHE A1392 TRP 0.004 0.001 TRP A1578 HIS 0.001 0.000 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 9029) covalent geometry : angle 0.51823 / 0.28 (12339) hydrogen bonds : bond 0.04521 / 3.05 ( 507) hydrogen bonds : angle 4.31669 / 3.11 ( 1424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.271 Fit side-chains REVERT: A 1416 MET cc_start: 0.8726 (mtp) cc_final: 0.8431 (mtt) REVERT: A 1480 MET cc_start: 0.9136 (tmm) cc_final: 0.8787 (tmm) REVERT: A 1533 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8781 (tpt) REVERT: A 1696 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 1710 ASN cc_start: 0.8972 (m-40) cc_final: 0.8623 (p0) REVERT: A 1869 MET cc_start: 0.6521 (mmp) cc_final: 0.6141 (mmt) REVERT: A 1886 GLU cc_start: 0.9132 (tp30) cc_final: 0.8667 (tp30) REVERT: A 2075 MET cc_start: 0.8516 (mtt) cc_final: 0.8183 (mtm) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 0.5713 time to fit residues: 31.9003 Evaluate side-chains 51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1739 MET Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048570 restraints weight = 26445.718| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.98 r_work: 0.2568 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9029 Z= 0.132 Angle : 0.514 8.154 12339 Z= 0.270 Chirality : 0.041 0.382 1421 Planarity : 0.003 0.041 1523 Dihedral : 16.380 172.453 1442 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.35 % Allowed : 10.95 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.42 (0.26), residues: 1088 helix: 2.81 (0.21), residues: 623 sheet: -0.41 (0.59), residues: 79 loop : 0.04 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1315 TYR 0.007 0.001 TYR A1984 PHE 0.012 0.001 PHE A1392 TRP 0.003 0.001 TRP A1578 HIS 0.001 0.000 HIS A1340 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9029) covalent geometry : angle 0.51422 / 0.27 (12339) hydrogen bonds : bond 0.04230 / 2.84 ( 507) hydrogen bonds : angle 4.20501 / 3.03 ( 1424) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.308 Fit side-chains REVERT: A 1480 MET cc_start: 0.9109 (tmm) cc_final: 0.8700 (tmm) REVERT: A 1533 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8810 (tpt) REVERT: A 1696 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 1710 ASN cc_start: 0.8969 (m-40) cc_final: 0.8630 (p0) REVERT: A 1869 MET cc_start: 0.6558 (mmp) cc_final: 0.6160 (mmt) REVERT: A 1886 GLU cc_start: 0.9124 (tp30) cc_final: 0.8698 (tm-30) REVERT: A 2075 MET cc_start: 0.8499 (mtt) cc_final: 0.8166 (mtm) outliers start: 12 outliers final: 3 residues processed: 57 average time/residue: 0.5717 time to fit residues: 34.9820 Evaluate side-chains 51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 48 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.049652 restraints weight = 26150.142| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.92 r_work: 0.2556 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9029 Z= 0.103 Angle : 0.489 7.634 12339 Z= 0.258 Chirality : 0.040 0.359 1421 Planarity : 0.003 0.041 1523 Dihedral : 16.303 169.653 1442 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.13 % Allowed : 11.96 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.50 (0.26), residues: 1088 helix: 2.85 (0.21), residues: 626 sheet: -0.43 (0.58), residues: 79 loop : 0.12 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1315 TYR 0.010 0.001 TYR A1984 PHE 0.010 0.001 PHE A2088 TRP 0.003 0.001 TRP A1578 HIS 0.001 0.000 HIS A2044 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 ( 9029) covalent geometry : angle 0.48916 / 0.26 (12339) hydrogen bonds : bond 0.03655 / 2.47 ( 507) hydrogen bonds : angle 4.06421 / 2.93 ( 1424) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.230 Fit side-chains REVERT: A 1480 MET cc_start: 0.9030 (tmm) cc_final: 0.8678 (tmm) REVERT: A 1533 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8623 (tpt) REVERT: A 1696 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 1710 ASN cc_start: 0.9079 (m-40) cc_final: 0.8724 (p0) REVERT: A 1869 MET cc_start: 0.6488 (mmp) cc_final: 0.6054 (mmt) REVERT: A 1886 GLU cc_start: 0.9060 (tp30) cc_final: 0.8610 (tm-30) REVERT: A 2075 MET cc_start: 0.8310 (mtt) cc_final: 0.7991 (mtm) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.4296 time to fit residues: 27.2396 Evaluate side-chains 53 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.048304 restraints weight = 26371.320| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.93 r_work: 0.2568 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 0.031 9029 Z= 0.159 Angle : 0.526 9.234 12339 Z= 0.274 Chirality : 0.042 0.373 1421 Planarity : 0.003 0.040 1523 Dihedral : 16.292 168.543 1442 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.24 % Allowed : 12.64 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.50 (0.26), residues: 1088 helix: 2.88 (0.21), residues: 624 sheet: -0.40 (0.59), residues: 79 loop : 0.05 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1315 TYR 0.010 0.001 TYR A1984 PHE 0.011 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.001 0.000 HIS A1788 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9029) covalent geometry : angle 0.52618 / 0.27 (12339) hydrogen bonds : bond 0.03988 / 2.69 ( 507) hydrogen bonds : angle 4.10421 / 2.96 ( 1424) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.298 Fit side-chains REVERT: A 1392 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 1480 MET cc_start: 0.9090 (tmm) cc_final: 0.8685 (tmm) REVERT: A 1533 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8759 (tpt) REVERT: A 1696 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 1710 ASN cc_start: 0.9034 (m-40) cc_final: 0.8728 (p0) REVERT: A 1869 MET cc_start: 0.6564 (mmp) cc_final: 0.6186 (mmt) REVERT: A 1886 GLU cc_start: 0.9114 (tp30) cc_final: 0.8663 (tm-30) REVERT: A 2075 MET cc_start: 0.8471 (mtt) cc_final: 0.8132 (mtm) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.4280 time to fit residues: 25.8070 Evaluate side-chains 55 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1392 PHE Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.048053 restraints weight = 26142.054| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.89 r_work: 0.2563 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9029 Z= 0.161 Angle : 0.519 8.600 12339 Z= 0.272 Chirality : 0.042 0.367 1421 Planarity : 0.003 0.040 1523 Dihedral : 16.266 167.073 1442 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.79 % Allowed : 13.32 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.48 (0.26), residues: 1088 helix: 2.90 (0.21), residues: 622 sheet: -0.44 (0.59), residues: 79 loop : 0.00 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1315 TYR 0.008 0.001 TYR A1984 PHE 0.012 0.001 PHE A1392 TRP 0.005 0.001 TRP A1159 HIS 0.001 0.000 HIS A1788 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9029) covalent geometry : angle 0.51878 / 0.27 (12339) hydrogen bonds : bond 0.04072 / 2.75 ( 507) hydrogen bonds : angle 4.09552 / 2.95 ( 1424) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.336 Fit side-chains REVERT: A 1480 MET cc_start: 0.9095 (tmm) cc_final: 0.8691 (tmm) REVERT: A 1533 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8748 (tpt) REVERT: A 1696 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 1698 MET cc_start: 0.9103 (mmt) cc_final: 0.8867 (mmm) REVERT: A 1710 ASN cc_start: 0.9049 (m-40) cc_final: 0.8753 (p0) REVERT: A 1869 MET cc_start: 0.6593 (mmp) cc_final: 0.6237 (mmt) REVERT: A 1886 GLU cc_start: 0.9121 (tp30) cc_final: 0.8674 (tm-30) REVERT: A 2075 MET cc_start: 0.8483 (mtt) cc_final: 0.8169 (mtm) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.6064 time to fit residues: 36.3527 Evaluate side-chains 53 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 96 optimal weight: 4.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.049277 restraints weight = 26055.304| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.89 r_work: 0.2594 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9029 Z= 0.109 Angle : 0.502 9.258 12339 Z= 0.262 Chirality : 0.041 0.351 1421 Planarity : 0.003 0.041 1523 Dihedral : 16.241 166.351 1442 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.02 % Allowed : 13.21 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.52 (0.26), residues: 1088 helix: 2.90 (0.21), residues: 626 sheet: -0.39 (0.60), residues: 79 loop : 0.05 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1315 TYR 0.014 0.001 TYR A1984 PHE 0.009 0.001 PHE A2088 TRP 0.003 0.000 TRP A1578 HIS 0.001 0.000 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 9029) covalent geometry : angle 0.50217 / 0.26 (12339) hydrogen bonds : bond 0.03709 / 2.52 ( 507) hydrogen bonds : angle 4.01973 / 2.91 ( 1424) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.322 Fit side-chains REVERT: A 1480 MET cc_start: 0.9094 (tmm) cc_final: 0.8749 (tmm) REVERT: A 1533 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8676 (tpt) REVERT: A 1696 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 1710 ASN cc_start: 0.9042 (m-40) cc_final: 0.8748 (p0) REVERT: A 1869 MET cc_start: 0.6499 (mmp) cc_final: 0.6135 (mmt) REVERT: A 1886 GLU cc_start: 0.9105 (tp30) cc_final: 0.8647 (tm-30) REVERT: A 2075 MET cc_start: 0.8475 (mtt) cc_final: 0.8159 (mtm) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.5556 time to fit residues: 33.3531 Evaluate side-chains 54 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049521 restraints weight = 25983.808| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.91 r_work: 0.2576 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9029 Z= 0.108 Angle : 0.489 8.798 12339 Z= 0.257 Chirality : 0.040 0.342 1421 Planarity : 0.003 0.041 1523 Dihedral : 16.212 165.914 1442 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 13.43 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.53 (0.26), residues: 1088 helix: 2.91 (0.21), residues: 626 sheet: -0.43 (0.60), residues: 79 loop : 0.06 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1315 TYR 0.014 0.001 TYR A1984 PHE 0.011 0.001 PHE A1194 TRP 0.003 0.000 TRP A1578 HIS 0.001 0.000 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9029) covalent geometry : angle 0.48908 / 0.26 (12339) hydrogen bonds : bond 0.03574 / 2.42 ( 507) hydrogen bonds : angle 3.95725 / 2.86 ( 1424) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.199 Fit side-chains REVERT: A 1256 MET cc_start: 0.8089 (mmp) cc_final: 0.7773 (mmt) REVERT: A 1480 MET cc_start: 0.9062 (tmm) cc_final: 0.8708 (tmm) REVERT: A 1533 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8650 (tpt) REVERT: A 1696 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 1698 MET cc_start: 0.9085 (mmt) cc_final: 0.8840 (mmm) REVERT: A 1710 ASN cc_start: 0.9087 (m-40) cc_final: 0.8746 (p0) REVERT: A 1869 MET cc_start: 0.6505 (mmp) cc_final: 0.6131 (mmt) REVERT: A 1886 GLU cc_start: 0.9086 (tp30) cc_final: 0.8624 (tm-30) REVERT: A 2075 MET cc_start: 0.8444 (mtt) cc_final: 0.8143 (mtm) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.4324 time to fit residues: 26.5463 Evaluate side-chains 56 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1567 MET Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 2050 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 6 optimal weight: 0.0050 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049922 restraints weight = 25882.559| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.91 r_work: 0.2564 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9029 Z= 0.104 Angle : 0.493 9.730 12339 Z= 0.257 Chirality : 0.040 0.331 1421 Planarity : 0.003 0.041 1523 Dihedral : 16.176 165.278 1442 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.02 % Allowed : 13.54 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.53 (0.26), residues: 1088 helix: 2.91 (0.21), residues: 627 sheet: -0.47 (0.60), residues: 79 loop : 0.05 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1315 TYR 0.013 0.001 TYR A1984 PHE 0.010 0.001 PHE A2088 TRP 0.003 0.000 TRP A1578 HIS 0.001 0.000 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 9029) covalent geometry : angle 0.49274 / 0.26 (12339) hydrogen bonds : bond 0.03405 / 2.32 ( 507) hydrogen bonds : angle 3.91697 / 2.83 ( 1424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.37 seconds wall clock time: 33 minutes 35.36 seconds (2015.36 seconds total)