Starting phenix.real_space_refine on Thu Jul 2 10:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.map" model { file = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2026/7vg2_31963.cif" } resolution = 3.1 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= 0.007 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 71 5.49 5 S 35 5.16 5 C 4939 2.51 5 N 1402 2.21 5 O 1753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8203 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6695 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 38, 'TRANS': 806} Chain breaks: 7 Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 743 Classifications: {'RNA': 35} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 2, 'rna3p': 32} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 762 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3250 SG CYS A1091 80.111 40.909 60.628 1.00 37.81 S ATOM 3265 SG CYS A1093 77.913 44.550 59.990 1.00 40.00 S ATOM 3469 SG CYS A1119 77.965 41.631 57.831 1.00 29.71 S Time building chain proxies: 1.28, per 1000 atoms: 0.16 Number of scatterers: 8203 At special positions: 0 Unit cell: (116.6, 107.8, 97.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 35 16.00 P 71 15.00 O 1753 8.00 N 1402 7.00 C 4939 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: 0.62 Conformation dependent library (CDL) restraints added in 193.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A1123 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1119 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1093 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1091 " Number of angles added : 3 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 43.4% alpha, 9.7% beta 29 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 710 through 729 Processing helix chain 'A' and resid 778 through 795 removed outlier: 3.711A pdb=" N ILE A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.812A pdb=" N TYR A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 983 Processing helix chain 'A' and resid 992 through 1000 Processing helix chain 'A' and resid 1011 through 1034 Processing helix chain 'A' and resid 1038 through 1050 Processing helix chain 'A' and resid 1051 through 1061 Processing helix chain 'A' and resid 1128 through 1159 removed outlier: 3.836A pdb=" N SER A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A1148 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1150 " --> pdb=" O GLY A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1174 removed outlier: 3.891A pdb=" N VAL A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1196 removed outlier: 3.643A pdb=" N GLU A1190 " --> pdb=" O ASP A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1210 Processing helix chain 'A' and resid 1211 through 1215 Processing helix chain 'A' and resid 1220 through 1243 removed outlier: 3.627A pdb=" N SER A1229 " --> pdb=" O PHE A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.647A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 Processing helix chain 'A' and resid 1272 through 1276 removed outlier: 4.069A pdb=" N THR A1275 " --> pdb=" O ASN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 Processing helix chain 'A' and resid 1311 through 1329 removed outlier: 4.232A pdb=" N GLY A1315 " --> pdb=" O PRO A1311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 Processing helix chain 'A' and resid 1356 through 1369 Processing helix chain 'A' and resid 1405 through 1422 Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1544 through 1563 removed outlier: 3.680A pdb=" N SER A1548 " --> pdb=" O ASP A1544 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1549 " --> pdb=" O LYS A1545 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1107 through 1108 Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 691 removed outlier: 5.545A pdb=" N ALA A 654 " --> pdb=" O CYS A 704 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN A 706 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE A 652 " --> pdb=" O GLN A 706 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 828 through 829 Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 941 removed outlier: 6.427A pdb=" N LYS A 903 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE A 856 " --> pdb=" O LYS A 903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1372 through 1377 Processing sheet with id=AA6, first strand: chain 'A' and resid 1494 through 1496 removed outlier: 3.636A pdb=" N VAL A1535 " --> pdb=" O LEU A1527 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1631 1.32 - 1.45: 2389 1.45 - 1.57: 4301 1.57 - 1.69: 139 1.69 - 1.81: 52 Bond restraints: 8512 Sorted by residual: bond pdb=" P A C 1 " pdb=" OP3 A C 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB THR A1236 " pdb=" CG2 THR A1236 " ideal model delta sigma weight residual 1.521 1.380 0.141 3.30e-02 9.18e+02 1.82e+01 bond pdb=" SD MET A1011 " pdb=" CE MET A1011 " ideal model delta sigma weight residual 1.791 1.701 0.090 2.50e-02 1.60e+03 1.29e+01 bond pdb=" CB ARG A1062 " pdb=" CG ARG A1062 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.27e+01 bond pdb=" CB ASN A 726 " pdb=" CG ASN A 726 " ideal model delta sigma weight residual 1.516 1.429 0.087 2.50e-02 1.60e+03 1.22e+01 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10417 2.06 - 4.13: 1201 4.13 - 6.19: 163 6.19 - 8.25: 52 8.25 - 10.31: 12 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA ASN A1405 " pdb=" CB ASN A1405 " pdb=" CG ASN A1405 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.71e+01 angle pdb=" N PRO A1006 " pdb=" CA PRO A1006 " pdb=" C PRO A1006 " ideal model delta sigma weight residual 110.95 103.02 7.93 1.62e+00 3.81e-01 2.40e+01 angle pdb=" C THR A1404 " pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N GLY A 649 " pdb=" CA GLY A 649 " pdb=" C GLY A 649 " ideal model delta sigma weight residual 111.36 116.80 -5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" C LEU A 763 " pdb=" CA LEU A 763 " pdb=" CB LEU A 763 " ideal model delta sigma weight residual 109.75 117.22 -7.47 1.65e+00 3.67e-01 2.05e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 4504 15.87 - 31.74: 362 31.74 - 47.61: 94 47.61 - 63.47: 28 63.47 - 79.34: 5 Dihedral angle restraints: 4993 sinusoidal: 2528 harmonic: 2465 Sorted by residual: dihedral pdb=" CA PHE A1164 " pdb=" C PHE A1164 " pdb=" N ASP A1165 " pdb=" CA ASP A1165 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASP A1165 " pdb=" C ASP A1165 " pdb=" N PRO A1166 " pdb=" CA PRO A1166 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY A1310 " pdb=" C GLY A1310 " pdb=" N PRO A1311 " pdb=" CA PRO A1311 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 4990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1097 0.096 - 0.191: 260 0.191 - 0.287: 30 0.287 - 0.382: 7 0.382 - 0.478: 5 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU A1556 " pdb=" CB LEU A1556 " pdb=" CD1 LEU A1556 " pdb=" CD2 LEU A1556 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CB VAL A1374 " pdb=" CA VAL A1374 " pdb=" CG1 VAL A1374 " pdb=" CG2 VAL A1374 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA LEU A 763 " pdb=" N LEU A 763 " pdb=" C LEU A 763 " pdb=" CB LEU A 763 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1396 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " -0.042 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR A1142 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 19 " -0.047 2.00e-02 2.50e+03 3.03e-02 2.07e+01 pdb=" N1 U C 19 " 0.075 2.00e-02 2.50e+03 pdb=" C2 U C 19 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C 19 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 19 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U C 19 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U C 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U C 19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1243 " -0.043 2.00e-02 2.50e+03 3.02e-02 1.82e+01 pdb=" CG TYR A1243 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A1243 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A1243 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A1243 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A1243 " -0.005 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 38 2.44 - 3.05: 5021 3.05 - 3.67: 14133 3.67 - 4.28: 21155 4.28 - 4.90: 32202 Nonbonded interactions: 72549 Sorted by model distance: nonbonded pdb=" OD1 ASP A1316 " pdb="CA CA A2002 " model vdw 1.822 2.510 nonbonded pdb=" OE1 GLU A1136 " pdb="CA CA A2001 " model vdw 2.072 2.510 nonbonded pdb=" OE1 GLU A1224 " pdb=" OD1 ASP A1316 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP A1228 " pdb=" OE2 GLU A1319 " model vdw 2.208 3.040 nonbonded pdb=" OP1 U C 25 " pdb="CA CA A2002 " model vdw 2.208 2.510 ... (remaining 72544 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: 0.310 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.016 0.141 8516 Z= 0.741 Angle : 1.450 15.954 11848 Z= 0.817 Chirality : 0.086 0.478 1399 Planarity : 0.010 0.075 1251 Dihedral : 12.864 79.342 3389 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.96 % Favored : 91.80 % Rotamer: Outliers : 1.74 % Allowed : 7.61 % Favored : 90.65 % Cbeta Deviations : 0.12 % 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: -3.84 (0.23), residues: 829 helix: -2.53 (0.20), residues: 344 sheet: -2.14 (0.42), residues: 127 loop : -2.57 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 968 TYR 0.076 0.008 TYR A1142 PHE 0.044 0.007 PHE A 745 TRP 0.031 0.007 TRP A1078 HIS 0.016 0.005 HIS A1153 Details of bonding type rmsd/Z covalent geometry : bond 0.01625 / 0.74 ( 8512) covalent geometry : angle 1.43177 / 0.82 (11845) hydrogen bonds : bond 0.16027 / 10.94 ( 378) hydrogen bonds : angle 8.14039 / 5.44 ( 1027) metal coordination : bond 0.09249 / 4.64 ( 4) metal coordination : angle 14.37720 / 7.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 694 ARG cc_start: 0.6876 (mmp80) cc_final: 0.6627 (mmp80) REVERT: A 734 VAL cc_start: 0.8509 (p) cc_final: 0.7764 (m) REVERT: A 841 GLU cc_start: 0.6559 (pp20) cc_final: 0.6295 (pp20) REVERT: A 860 VAL cc_start: 0.6086 (t) cc_final: 0.5857 (m) REVERT: A 1145 SER cc_start: 0.8398 (m) cc_final: 0.8136 (m) REVERT: A 1283 VAL cc_start: 0.8676 (p) cc_final: 0.8466 (m) REVERT: A 1472 MET cc_start: 0.5510 (mmt) cc_final: 0.5079 (mmt) outliers start: 13 outliers final: 5 residues processed: 142 average time/residue: 0.0827 time to fit residues: 15.6224 Evaluate side-chains 102 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1537 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 HIS A1029 HIS A1197 HIS A1241 ASN A1278 GLN A1378 ASN A1488 HIS A1569 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124122 restraints weight = 10374.264| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.67 r_work: 0.3243 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8516 Z= 0.159 Angle : 0.678 9.208 11848 Z= 0.349 Chirality : 0.040 0.190 1399 Planarity : 0.005 0.051 1251 Dihedral : 9.303 61.364 1758 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 3.60 % Allowed : 9.35 % Favored : 87.05 % 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: -2.06 (0.26), residues: 829 helix: -0.66 (0.23), residues: 351 sheet: -1.80 (0.44), residues: 128 loop : -1.82 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1098 TYR 0.018 0.002 TYR A1142 PHE 0.014 0.002 PHE A 724 TRP 0.013 0.002 TRP A 779 HIS 0.005 0.001 HIS A1276 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 8512) covalent geometry : angle 0.67653 / 0.35 (11845) hydrogen bonds : bond 0.04638 / 3.10 ( 378) hydrogen bonds : angle 5.37655 / 3.59 ( 1027) metal coordination : bond 0.00859 / 0.43 ( 4) metal coordination : angle 2.51239 / 1.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.271 Fit side-chains REVERT: A 734 VAL cc_start: 0.8040 (p) cc_final: 0.7318 (m) REVERT: A 756 HIS cc_start: 0.8195 (m90) cc_final: 0.7990 (m-70) REVERT: A 841 GLU cc_start: 0.6887 (pp20) cc_final: 0.6354 (pp20) REVERT: A 1019 ASP cc_start: 0.7730 (t0) cc_final: 0.7182 (t70) REVERT: A 1038 ASP cc_start: 0.8244 (p0) cc_final: 0.7973 (p0) REVERT: A 1085 SER cc_start: 0.8711 (m) cc_final: 0.8373 (p) REVERT: A 1145 SER cc_start: 0.8267 (m) cc_final: 0.8030 (m) REVERT: A 1192 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 1202 LYS cc_start: 0.7818 (mttp) cc_final: 0.7257 (mmtt) REVERT: A 1338 ARG cc_start: 0.6760 (ttp80) cc_final: 0.6293 (ttm-80) REVERT: A 1406 LYS cc_start: 0.8091 (tppp) cc_final: 0.7762 (ttmt) REVERT: A 1528 ARG cc_start: 0.7679 (mpp80) cc_final: 0.6400 (mmm160) outliers start: 27 outliers final: 15 residues processed: 144 average time/residue: 0.0845 time to fit residues: 16.9137 Evaluate side-chains 116 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1535 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1196 GLN A1211 HIS ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126065 restraints weight = 10117.997| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.53 r_work: 0.3255 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8516 Z= 0.202 Angle : 0.676 9.772 11848 Z= 0.343 Chirality : 0.041 0.293 1399 Planarity : 0.005 0.056 1251 Dihedral : 8.728 57.698 1754 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 4.67 % Allowed : 11.75 % Favored : 83.58 % 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: -1.24 (0.28), residues: 829 helix: 0.19 (0.25), residues: 353 sheet: -1.62 (0.46), residues: 129 loop : -1.48 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1098 TYR 0.018 0.002 TYR A1142 PHE 0.017 0.002 PHE A1203 TRP 0.009 0.002 TRP A1125 HIS 0.006 0.001 HIS A1276 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 8512) covalent geometry : angle 0.67475 / 0.34 (11845) hydrogen bonds : bond 0.04530 / 3.01 ( 378) hydrogen bonds : angle 5.00851 / 3.35 ( 1027) metal coordination : bond 0.00648 / 0.32 ( 4) metal coordination : angle 2.35639 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.225 Fit side-chains REVERT: A 734 VAL cc_start: 0.8248 (p) cc_final: 0.7627 (m) REVERT: A 841 GLU cc_start: 0.6925 (pp20) cc_final: 0.6348 (pp20) REVERT: A 1003 LEU cc_start: 0.8980 (tp) cc_final: 0.8766 (mt) REVERT: A 1019 ASP cc_start: 0.7623 (t0) cc_final: 0.7140 (t70) REVERT: A 1164 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.5813 (t80) REVERT: A 1202 LYS cc_start: 0.7914 (mttp) cc_final: 0.7415 (mmtt) REVERT: A 1224 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: A 1338 ARG cc_start: 0.6635 (ttp80) cc_final: 0.6196 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7122 (mp) REVERT: A 1528 ARG cc_start: 0.7667 (mpp80) cc_final: 0.6337 (mmm160) outliers start: 35 outliers final: 23 residues processed: 128 average time/residue: 0.0847 time to fit residues: 14.9379 Evaluate side-chains 123 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124156 restraints weight = 10420.580| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.56 r_work: 0.3221 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8516 Z= 0.197 Angle : 0.659 10.005 11848 Z= 0.334 Chirality : 0.040 0.220 1399 Planarity : 0.005 0.057 1251 Dihedral : 8.515 57.285 1753 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 5.21 % Allowed : 14.95 % Favored : 79.84 % 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: -0.87 (0.28), residues: 829 helix: 0.56 (0.26), residues: 353 sheet: -1.47 (0.46), residues: 127 loop : -1.35 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1098 TYR 0.017 0.002 TYR A1220 PHE 0.016 0.002 PHE A1203 TRP 0.008 0.001 TRP A1125 HIS 0.010 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 8512) covalent geometry : angle 0.65782 / 0.33 (11845) hydrogen bonds : bond 0.04392 / 2.91 ( 378) hydrogen bonds : angle 4.86302 / 3.24 ( 1027) metal coordination : bond 0.00562 / 0.28 ( 4) metal coordination : angle 2.30773 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.267 Fit side-chains REVERT: A 734 VAL cc_start: 0.8227 (p) cc_final: 0.7636 (m) REVERT: A 841 GLU cc_start: 0.7015 (pp20) cc_final: 0.6456 (pp20) REVERT: A 1164 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.5933 (t80) REVERT: A 1202 LYS cc_start: 0.7894 (mttp) cc_final: 0.7340 (mmtt) REVERT: A 1224 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: A 1276 HIS cc_start: 0.7919 (m-70) cc_final: 0.7690 (m-70) REVERT: A 1417 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 1528 ARG cc_start: 0.7648 (mpp80) cc_final: 0.6304 (mmm160) outliers start: 39 outliers final: 29 residues processed: 125 average time/residue: 0.0857 time to fit residues: 14.8469 Evaluate side-chains 124 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 0.0770 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127743 restraints weight = 10323.001| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.56 r_work: 0.3268 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8516 Z= 0.150 Angle : 0.608 10.194 11848 Z= 0.307 Chirality : 0.038 0.180 1399 Planarity : 0.004 0.052 1251 Dihedral : 8.283 59.988 1753 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Rotamer: Outliers : 5.34 % Allowed : 15.75 % Favored : 78.91 % 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: -0.45 (0.29), residues: 829 helix: 0.86 (0.26), residues: 362 sheet: -1.09 (0.49), residues: 108 loop : -1.21 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1515 TYR 0.015 0.002 TYR A1220 PHE 0.015 0.002 PHE A1203 TRP 0.007 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8512) covalent geometry : angle 0.60731 / 0.31 (11845) hydrogen bonds : bond 0.04117 / 2.72 ( 378) hydrogen bonds : angle 4.67359 / 3.11 ( 1027) metal coordination : bond 0.00380 / 0.19 ( 4) metal coordination : angle 1.63539 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.265 Fit side-chains REVERT: A 666 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: A 734 VAL cc_start: 0.8187 (p) cc_final: 0.7627 (m) REVERT: A 788 ILE cc_start: 0.8381 (tp) cc_final: 0.8174 (tp) REVERT: A 841 GLU cc_start: 0.7036 (pp20) cc_final: 0.6490 (pp20) REVERT: A 852 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7760 (ptp-170) REVERT: A 1164 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.5997 (t80) REVERT: A 1202 LYS cc_start: 0.7834 (mttp) cc_final: 0.7558 (mmtt) REVERT: A 1276 HIS cc_start: 0.7945 (m-70) cc_final: 0.7731 (m-70) REVERT: A 1338 ARG cc_start: 0.6687 (ttp80) cc_final: 0.6154 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6856 (mp) REVERT: A 1528 ARG cc_start: 0.7581 (mpp80) cc_final: 0.6233 (mmm160) outliers start: 40 outliers final: 30 residues processed: 135 average time/residue: 0.1097 time to fit residues: 19.7460 Evaluate side-chains 130 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130881 restraints weight = 10163.439| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.52 r_work: 0.3291 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8516 Z= 0.143 Angle : 0.600 10.255 11848 Z= 0.303 Chirality : 0.038 0.172 1399 Planarity : 0.004 0.049 1251 Dihedral : 8.089 59.000 1751 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 6.01 % Allowed : 16.15 % Favored : 77.84 % 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: -0.23 (0.29), residues: 829 helix: 1.03 (0.27), residues: 364 sheet: -1.04 (0.49), residues: 108 loop : -1.07 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1515 TYR 0.014 0.002 TYR A1220 PHE 0.013 0.002 PHE A1203 TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8512) covalent geometry : angle 0.60010 / 0.30 (11845) hydrogen bonds : bond 0.04024 / 2.66 ( 378) hydrogen bonds : angle 4.56015 / 3.03 ( 1027) metal coordination : bond 0.00359 / 0.18 ( 4) metal coordination : angle 1.45750 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.274 Fit side-chains REVERT: A 666 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6831 (pp20) REVERT: A 734 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7651 (m) REVERT: A 788 ILE cc_start: 0.8360 (tp) cc_final: 0.8151 (tp) REVERT: A 953 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7460 (ttt90) REVERT: A 998 GLU cc_start: 0.7956 (tt0) cc_final: 0.7620 (tt0) REVERT: A 1019 ASP cc_start: 0.7706 (t70) cc_final: 0.7330 (t70) REVERT: A 1202 LYS cc_start: 0.7843 (mttp) cc_final: 0.7601 (mmtt) REVERT: A 1338 ARG cc_start: 0.6669 (ttp80) cc_final: 0.6130 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6825 (mp) REVERT: A 1528 ARG cc_start: 0.7477 (mpp80) cc_final: 0.6286 (mmm160) REVERT: A 1564 LYS cc_start: 0.6874 (mmtp) cc_final: 0.6216 (mmmm) outliers start: 45 outliers final: 30 residues processed: 136 average time/residue: 0.0994 time to fit residues: 18.1718 Evaluate side-chains 127 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127459 restraints weight = 10345.023| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.60 r_work: 0.3286 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8516 Z= 0.146 Angle : 0.607 10.223 11848 Z= 0.304 Chirality : 0.038 0.273 1399 Planarity : 0.004 0.049 1251 Dihedral : 8.017 58.709 1751 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 5.34 % Allowed : 16.96 % Favored : 77.70 % 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: -0.05 (0.29), residues: 829 helix: 1.14 (0.27), residues: 363 sheet: -0.87 (0.49), residues: 106 loop : -0.95 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1515 TYR 0.014 0.002 TYR A 854 PHE 0.014 0.002 PHE A 724 TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8512) covalent geometry : angle 0.60687 / 0.30 (11845) hydrogen bonds : bond 0.04026 / 2.66 ( 378) hydrogen bonds : angle 4.55246 / 3.03 ( 1027) metal coordination : bond 0.00314 / 0.16 ( 4) metal coordination : angle 1.39183 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.273 Fit side-chains REVERT: A 666 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6800 (pp20) REVERT: A 734 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 767 GLU cc_start: 0.6257 (tp30) cc_final: 0.5892 (tp30) REVERT: A 953 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7398 (ttt90) REVERT: A 998 GLU cc_start: 0.8014 (tt0) cc_final: 0.7677 (tt0) REVERT: A 1019 ASP cc_start: 0.7633 (t70) cc_final: 0.7246 (t0) REVERT: A 1202 LYS cc_start: 0.7769 (mttp) cc_final: 0.7521 (mmtt) REVERT: A 1338 ARG cc_start: 0.6729 (ttp80) cc_final: 0.6166 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6838 (mp) REVERT: A 1528 ARG cc_start: 0.7627 (mpp80) cc_final: 0.6210 (mmm160) REVERT: A 1564 LYS cc_start: 0.6911 (mmtp) cc_final: 0.6162 (mmmm) outliers start: 40 outliers final: 31 residues processed: 130 average time/residue: 0.0992 time to fit residues: 17.3966 Evaluate side-chains 130 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126738 restraints weight = 10274.525| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.60 r_work: 0.3274 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8516 Z= 0.150 Angle : 0.605 10.267 11848 Z= 0.303 Chirality : 0.038 0.242 1399 Planarity : 0.004 0.063 1251 Dihedral : 7.975 58.794 1751 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 5.74 % Allowed : 17.49 % Favored : 76.77 % 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: -0.01 (0.29), residues: 829 helix: 1.24 (0.27), residues: 358 sheet: -0.94 (0.49), residues: 108 loop : -0.94 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1515 TYR 0.014 0.002 TYR A1220 PHE 0.013 0.002 PHE A1203 TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8512) covalent geometry : angle 0.60498 / 0.30 (11845) hydrogen bonds : bond 0.04007 / 2.65 ( 378) hydrogen bonds : angle 4.54801 / 3.03 ( 1027) metal coordination : bond 0.00329 / 0.16 ( 4) metal coordination : angle 1.42739 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.274 Fit side-chains REVERT: A 666 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: A 734 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 841 GLU cc_start: 0.7112 (pp20) cc_final: 0.6709 (pp20) REVERT: A 953 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7432 (ttt90) REVERT: A 998 GLU cc_start: 0.8018 (tt0) cc_final: 0.7676 (tt0) REVERT: A 1019 ASP cc_start: 0.7637 (t70) cc_final: 0.7241 (t0) REVERT: A 1202 LYS cc_start: 0.7733 (mttp) cc_final: 0.7498 (mmtt) REVERT: A 1338 ARG cc_start: 0.6747 (ttp80) cc_final: 0.6187 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6829 (mp) REVERT: A 1528 ARG cc_start: 0.7422 (mpp80) cc_final: 0.6157 (mmm160) REVERT: A 1564 LYS cc_start: 0.6889 (mmtp) cc_final: 0.6168 (mmmm) outliers start: 43 outliers final: 35 residues processed: 132 average time/residue: 0.0985 time to fit residues: 17.7627 Evaluate side-chains 134 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129344 restraints weight = 10250.230| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.52 r_work: 0.3289 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8516 Z= 0.168 Angle : 0.623 9.852 11848 Z= 0.313 Chirality : 0.039 0.248 1399 Planarity : 0.004 0.069 1251 Dihedral : 8.002 59.676 1751 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.47 % Allowed : 18.42 % Favored : 76.10 % 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: 0.01 (0.29), residues: 829 helix: 1.16 (0.27), residues: 361 sheet: -0.77 (0.49), residues: 106 loop : -0.88 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1515 TYR 0.015 0.002 TYR A1220 PHE 0.014 0.002 PHE A 724 TRP 0.006 0.001 TRP A1125 HIS 0.012 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8512) covalent geometry : angle 0.62288 / 0.31 (11845) hydrogen bonds : bond 0.04094 / 2.71 ( 378) hydrogen bonds : angle 4.60387 / 3.06 ( 1027) metal coordination : bond 0.00382 / 0.19 ( 4) metal coordination : angle 1.79163 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.282 Fit side-chains REVERT: A 666 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: A 734 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7645 (m) REVERT: A 841 GLU cc_start: 0.7083 (pp20) cc_final: 0.6623 (pp20) REVERT: A 953 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7373 (ttt90) REVERT: A 1019 ASP cc_start: 0.7634 (t70) cc_final: 0.7243 (t0) REVERT: A 1202 LYS cc_start: 0.7876 (mttp) cc_final: 0.7594 (mmtt) REVERT: A 1338 ARG cc_start: 0.6777 (ttp80) cc_final: 0.6229 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6940 (mp) REVERT: A 1528 ARG cc_start: 0.7610 (mpp80) cc_final: 0.6241 (mmm160) REVERT: A 1564 LYS cc_start: 0.6782 (mmtp) cc_final: 0.6109 (mmmm) outliers start: 41 outliers final: 36 residues processed: 130 average time/residue: 0.1000 time to fit residues: 17.6914 Evaluate side-chains 136 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127523 restraints weight = 10168.147| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.57 r_work: 0.3290 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8516 Z= 0.158 Angle : 0.619 10.102 11848 Z= 0.311 Chirality : 0.039 0.238 1399 Planarity : 0.004 0.068 1251 Dihedral : 7.950 59.014 1751 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.21 % Allowed : 18.56 % Favored : 76.23 % 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: 0.05 (0.29), residues: 829 helix: 1.17 (0.27), residues: 361 sheet: -0.70 (0.49), residues: 106 loop : -0.87 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1532 TYR 0.014 0.002 TYR A1220 PHE 0.013 0.002 PHE A1203 TRP 0.007 0.001 TRP A1125 HIS 0.012 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 8512) covalent geometry : angle 0.61876 / 0.31 (11845) hydrogen bonds : bond 0.04036 / 2.67 ( 378) hydrogen bonds : angle 4.56955 / 3.04 ( 1027) metal coordination : bond 0.00353 / 0.18 ( 4) metal coordination : angle 1.52939 / 0.85 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.273 Fit side-chains REVERT: A 666 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6652 (pp20) REVERT: A 734 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7647 (m) REVERT: A 830 PHE cc_start: 0.8705 (m-80) cc_final: 0.8472 (m-80) REVERT: A 841 GLU cc_start: 0.7066 (pp20) cc_final: 0.6594 (pp20) REVERT: A 953 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7420 (ttt90) REVERT: A 1019 ASP cc_start: 0.7647 (t70) cc_final: 0.7250 (t0) REVERT: A 1202 LYS cc_start: 0.7796 (mttp) cc_final: 0.7541 (mmtt) REVERT: A 1338 ARG cc_start: 0.6746 (ttp80) cc_final: 0.6222 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6940 (mp) REVERT: A 1528 ARG cc_start: 0.7543 (mpp80) cc_final: 0.6228 (mmm160) REVERT: A 1564 LYS cc_start: 0.6847 (mmtp) cc_final: 0.6148 (mmmm) outliers start: 39 outliers final: 35 residues processed: 129 average time/residue: 0.1071 time to fit residues: 18.6640 Evaluate side-chains 136 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1041 GLN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1516 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123848 restraints weight = 10393.108| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.62 r_work: 0.3243 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8516 Z= 0.183 Angle : 0.637 9.959 11848 Z= 0.320 Chirality : 0.040 0.238 1399 Planarity : 0.004 0.070 1251 Dihedral : 7.961 59.266 1751 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.34 % Allowed : 18.56 % Favored : 76.10 % 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: 0.01 (0.29), residues: 829 helix: 1.10 (0.27), residues: 361 sheet: -0.64 (0.49), residues: 106 loop : -0.86 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1532 TYR 0.015 0.002 TYR A1220 PHE 0.014 0.002 PHE A1203 TRP 0.007 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 8512) covalent geometry : angle 0.63611 / 0.32 (11845) hydrogen bonds : bond 0.04156 / 2.75 ( 378) hydrogen bonds : angle 4.62816 / 3.08 ( 1027) metal coordination : bond 0.00440 / 0.22 ( 4) metal coordination : angle 2.03248 / 1.14 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.51 seconds wall clock time: 40 minutes 4.53 seconds (2404.53 seconds total)