Starting phenix.real_space_refine on Sat Jul 26 05:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_31963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_31963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_31963.map" model { file = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_31963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vg2_31963/07_2025/7vg2_31963.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.10, per 1000 atoms: 0.62 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: 2.32 Conformation dependent library (CDL) restraints added in 793.9 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: 3.31 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: 3.94 Time building geometry restraints manager: 2.69 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: 4572 15.87 - 31.74: 391 31.74 - 47.61: 132 47.61 - 63.47: 90 63.47 - 79.34: 36 Dihedral angle restraints: 5221 sinusoidal: 2756 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 5218 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: 0.300 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 16.555 79.342 3617 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.007 TRP A1078 HIS 0.016 0.005 HIS A1153 PHE 0.044 0.007 PHE A 745 TYR 0.076 0.008 TYR A1142 ARG 0.031 0.003 ARG A 968 Details of bonding type rmsd hydrogen bonds : bond 0.16027 ( 378) hydrogen bonds : angle 8.14039 ( 1027) metal coordination : bond 0.09249 ( 4) metal coordination : angle 14.37720 ( 3) covalent geometry : bond 0.01625 ( 8512) covalent geometry : angle 1.43177 (11845) *********************** 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 : 0.821 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: 0.2415 time to fit residues: 45.3595 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 : 0.827 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3654 r_free = 0.3654 target = 0.150172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123265 restraints weight = 10208.931| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.66 r_work: 0.3212 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8516 Z= 0.165 Angle : 0.686 9.286 11848 Z= 0.353 Chirality : 0.040 0.196 1399 Planarity : 0.005 0.051 1251 Dihedral : 17.319 74.074 1986 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 3.47 % Allowed : 9.35 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.26), residues: 829 helix: -0.67 (0.23), residues: 351 sheet: -1.80 (0.44), residues: 128 loop : -1.83 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 779 HIS 0.005 0.001 HIS A1276 PHE 0.014 0.002 PHE A 724 TYR 0.018 0.002 TYR A1142 ARG 0.006 0.001 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 378) hydrogen bonds : angle 5.37895 ( 1027) metal coordination : bond 0.00898 ( 4) metal coordination : angle 2.68523 ( 3) covalent geometry : bond 0.00351 ( 8512) covalent geometry : angle 0.68434 (11845) *********************** 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 150 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.843 Fit side-chains REVERT: A 734 VAL cc_start: 0.8026 (p) cc_final: 0.7305 (m) REVERT: A 756 HIS cc_start: 0.8186 (m90) cc_final: 0.7978 (m-70) REVERT: A 841 GLU cc_start: 0.6886 (pp20) cc_final: 0.6348 (pp20) REVERT: A 1019 ASP cc_start: 0.7735 (t0) cc_final: 0.7180 (t70) REVERT: A 1038 ASP cc_start: 0.8236 (p0) cc_final: 0.7964 (p0) REVERT: A 1085 SER cc_start: 0.8707 (m) cc_final: 0.8364 (p) REVERT: A 1145 SER cc_start: 0.8271 (m) cc_final: 0.8030 (m) REVERT: A 1202 LYS cc_start: 0.7816 (mttp) cc_final: 0.7337 (mmtt) REVERT: A 1338 ARG cc_start: 0.6740 (ttp80) cc_final: 0.6199 (ttm-80) REVERT: A 1528 ARG cc_start: 0.7674 (mpp80) cc_final: 0.6406 (mmm160) outliers start: 26 outliers final: 15 residues processed: 140 average time/residue: 0.1973 time to fit residues: 38.1465 Evaluate side-chains 119 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 84 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3623 r_free = 0.3623 target = 0.147560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120168 restraints weight = 10434.849| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.67 r_work: 0.3172 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2369 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= 0.197 Angle : 0.666 9.743 11848 Z= 0.340 Chirality : 0.040 0.266 1399 Planarity : 0.005 0.058 1251 Dihedral : 17.030 73.987 1982 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 4.54 % Allowed : 11.75 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 829 helix: 0.18 (0.25), residues: 353 sheet: -1.58 (0.46), residues: 127 loop : -1.50 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1125 HIS 0.006 0.001 HIS A1276 PHE 0.017 0.002 PHE A1203 TYR 0.017 0.002 TYR A1142 ARG 0.004 0.001 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 378) hydrogen bonds : angle 4.99828 ( 1027) metal coordination : bond 0.00606 ( 4) metal coordination : angle 2.29509 ( 3) covalent geometry : bond 0.00432 ( 8512) covalent geometry : angle 0.66545 (11845) *********************** 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 139 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.502 Fit side-chains REVERT: A 734 VAL cc_start: 0.8132 (p) cc_final: 0.7520 (m) REVERT: A 756 HIS cc_start: 0.8255 (m90) cc_final: 0.7961 (m90) REVERT: A 841 GLU cc_start: 0.6940 (pp20) cc_final: 0.6346 (pp20) REVERT: A 1003 LEU cc_start: 0.9006 (tp) cc_final: 0.8794 (mt) REVERT: A 1019 ASP cc_start: 0.7659 (t70) cc_final: 0.7163 (t70) REVERT: A 1085 SER cc_start: 0.8814 (m) cc_final: 0.8454 (p) REVERT: A 1164 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.5884 (t80) REVERT: A 1224 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 1338 ARG cc_start: 0.6709 (ttp80) cc_final: 0.6199 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 1528 ARG cc_start: 0.7675 (mpp80) cc_final: 0.6269 (mmm160) REVERT: A 1532 ARG cc_start: 0.6222 (ttm-80) cc_final: 0.6015 (mtp85) outliers start: 34 outliers final: 23 residues processed: 128 average time/residue: 0.2735 time to fit residues: 48.1803 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 : 0.753 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN A1419 GLN A1488 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127503 restraints weight = 10177.784| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.53 r_work: 0.3246 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2663 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= 0.172 Angle : 0.635 9.865 11848 Z= 0.322 Chirality : 0.039 0.209 1399 Planarity : 0.004 0.054 1251 Dihedral : 16.968 73.986 1981 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.15 % Favored : 93.73 % Rotamer: Outliers : 5.07 % Allowed : 14.42 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.29), residues: 829 helix: 0.63 (0.26), residues: 359 sheet: -1.46 (0.46), residues: 127 loop : -1.31 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.015 0.002 PHE A1203 TYR 0.016 0.002 TYR A1220 ARG 0.004 0.001 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 378) hydrogen bonds : angle 4.79382 ( 1027) metal coordination : bond 0.00485 ( 4) metal coordination : angle 1.93850 ( 3) covalent geometry : bond 0.00375 ( 8512) covalent geometry : angle 0.63466 (11845) *********************** 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: 38 poor density : 99 time to evaluate : 2.004 Fit side-chains REVERT: A 734 VAL cc_start: 0.8195 (p) cc_final: 0.7606 (m) REVERT: A 788 ILE cc_start: 0.8402 (tp) cc_final: 0.8193 (tp) REVERT: A 841 GLU cc_start: 0.7058 (pp20) cc_final: 0.6453 (pp20) REVERT: A 1085 SER cc_start: 0.8822 (m) cc_final: 0.8454 (p) REVERT: A 1164 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5943 (t80) REVERT: A 1202 LYS cc_start: 0.7899 (mttp) cc_final: 0.7337 (mmtt) REVERT: A 1224 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 1276 HIS cc_start: 0.7911 (m-70) cc_final: 0.7689 (m-70) REVERT: A 1338 ARG cc_start: 0.6613 (ttp80) cc_final: 0.6049 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7043 (mp) REVERT: A 1528 ARG cc_start: 0.7614 (mpp80) cc_final: 0.6294 (mmm160) REVERT: A 1532 ARG cc_start: 0.5926 (ttm-80) cc_final: 0.5648 (mtp85) outliers start: 38 outliers final: 26 residues processed: 126 average time/residue: 0.3785 time to fit residues: 67.6022 Evaluate side-chains 120 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 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 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 42 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132060 restraints weight = 10112.362| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.51 r_work: 0.3326 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8516 Z= 0.136 Angle : 0.593 10.681 11848 Z= 0.299 Chirality : 0.038 0.172 1399 Planarity : 0.004 0.050 1251 Dihedral : 16.861 74.028 1979 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 4.94 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 829 helix: 1.05 (0.27), residues: 357 sheet: -1.14 (0.49), residues: 108 loop : -1.23 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.014 0.002 PHE A1203 TYR 0.014 0.001 TYR A1220 ARG 0.004 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 378) hydrogen bonds : angle 4.55608 ( 1027) metal coordination : bond 0.00305 ( 4) metal coordination : angle 1.26219 ( 3) covalent geometry : bond 0.00289 ( 8512) covalent geometry : angle 0.59275 (11845) *********************** 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 142 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.805 Fit side-chains REVERT: A 666 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: A 734 VAL cc_start: 0.8193 (p) cc_final: 0.7653 (m) REVERT: A 788 ILE cc_start: 0.8361 (tp) cc_final: 0.8141 (tp) REVERT: A 841 GLU cc_start: 0.7024 (pp20) cc_final: 0.6464 (pp20) REVERT: A 998 GLU cc_start: 0.7941 (tt0) cc_final: 0.7595 (tt0) REVERT: A 1019 ASP cc_start: 0.7702 (t70) cc_final: 0.7289 (t70) REVERT: A 1085 SER cc_start: 0.8800 (m) cc_final: 0.8456 (p) REVERT: A 1164 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.5895 (t80) REVERT: A 1338 ARG cc_start: 0.6494 (ttp80) cc_final: 0.6021 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6865 (mp) REVERT: A 1528 ARG cc_start: 0.7489 (mpp80) cc_final: 0.6183 (mmm160) REVERT: A 1532 ARG cc_start: 0.5844 (ttm-80) cc_final: 0.5259 (mmt180) REVERT: A 1564 LYS cc_start: 0.6751 (mmtp) cc_final: 0.6012 (mmmm) outliers start: 37 outliers final: 25 residues processed: 132 average time/residue: 0.2514 time to fit residues: 43.8645 Evaluate side-chains 120 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127601 restraints weight = 10248.528| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.59 r_work: 0.3310 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8516 Z= 0.151 Angle : 0.608 10.107 11848 Z= 0.306 Chirality : 0.038 0.181 1399 Planarity : 0.004 0.051 1251 Dihedral : 16.770 74.103 1979 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 5.87 % Allowed : 16.02 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 829 helix: 1.05 (0.27), residues: 364 sheet: -1.27 (0.46), residues: 125 loop : -1.05 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.014 0.002 PHE A 724 TYR 0.014 0.002 TYR A1220 ARG 0.004 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 378) hydrogen bonds : angle 4.51256 ( 1027) metal coordination : bond 0.00388 ( 4) metal coordination : angle 1.60608 ( 3) covalent geometry : bond 0.00329 ( 8512) covalent geometry : angle 0.60788 (11845) *********************** 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 146 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.823 Fit side-chains REVERT: A 666 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6858 (pp20) REVERT: A 734 VAL cc_start: 0.8152 (p) cc_final: 0.7636 (m) REVERT: A 767 GLU cc_start: 0.6283 (tp30) cc_final: 0.5844 (tp30) REVERT: A 788 ILE cc_start: 0.8367 (tp) cc_final: 0.8161 (tp) REVERT: A 953 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7478 (ttt90) REVERT: A 998 GLU cc_start: 0.7987 (tt0) cc_final: 0.7649 (tt0) REVERT: A 1019 ASP cc_start: 0.7623 (t70) cc_final: 0.7227 (t70) REVERT: A 1338 ARG cc_start: 0.6714 (ttp80) cc_final: 0.6168 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6906 (mp) REVERT: A 1528 ARG cc_start: 0.7528 (mpp80) cc_final: 0.6171 (mmm160) REVERT: A 1532 ARG cc_start: 0.5791 (ttm-80) cc_final: 0.5544 (mtp85) REVERT: A 1564 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6148 (mmmm) outliers start: 44 outliers final: 33 residues processed: 136 average time/residue: 0.2313 time to fit residues: 42.1356 Evaluate side-chains 128 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 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 1535 VAL Chi-restraints excluded: chain A residue 1537 TYR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.155700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129778 restraints weight = 10247.478| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.58 r_work: 0.3349 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3227 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= 0.130 Angle : 0.593 10.579 11848 Z= 0.297 Chirality : 0.038 0.269 1399 Planarity : 0.004 0.049 1251 Dihedral : 16.775 74.104 1979 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 5.87 % Allowed : 16.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 829 helix: 1.29 (0.27), residues: 356 sheet: -1.04 (0.49), residues: 108 loop : -1.09 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1125 HIS 0.012 0.001 HIS A1274 PHE 0.012 0.001 PHE A1203 TYR 0.014 0.001 TYR A 854 ARG 0.003 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 378) hydrogen bonds : angle 4.46880 ( 1027) metal coordination : bond 0.00267 ( 4) metal coordination : angle 1.20884 ( 3) covalent geometry : bond 0.00277 ( 8512) covalent geometry : angle 0.59283 (11845) *********************** 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 137 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.829 Fit side-chains REVERT: A 629 GLU cc_start: 0.8557 (pt0) cc_final: 0.8295 (pt0) REVERT: A 666 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: A 734 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7620 (m) REVERT: A 767 GLU cc_start: 0.6434 (tp30) cc_final: 0.5959 (tp30) REVERT: A 788 ILE cc_start: 0.8357 (tp) cc_final: 0.8141 (tp) REVERT: A 953 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7486 (ttt90) REVERT: A 998 GLU cc_start: 0.7996 (tt0) cc_final: 0.7662 (tt0) REVERT: A 1019 ASP cc_start: 0.7624 (t70) cc_final: 0.7173 (t0) REVERT: A 1338 ARG cc_start: 0.6704 (ttp80) cc_final: 0.6140 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6911 (mp) REVERT: A 1472 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.1579 (ptm) REVERT: A 1528 ARG cc_start: 0.7542 (mpp80) cc_final: 0.6194 (mmm160) REVERT: A 1532 ARG cc_start: 0.5754 (ttm-80) cc_final: 0.5538 (mtp85) REVERT: A 1564 LYS cc_start: 0.6966 (mmtp) cc_final: 0.6182 (mmmm) outliers start: 44 outliers final: 32 residues processed: 126 average time/residue: 0.2322 time to fit residues: 39.1351 Evaluate side-chains 127 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 1232 ASP 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 1332 ASP 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 1472 MET 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 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129982 restraints weight = 10294.156| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.57 r_work: 0.3323 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8516 Z= 0.142 Angle : 0.596 10.675 11848 Z= 0.298 Chirality : 0.038 0.233 1399 Planarity : 0.004 0.049 1251 Dihedral : 16.698 74.095 1979 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 5.47 % Allowed : 16.96 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 829 helix: 1.30 (0.27), residues: 357 sheet: -0.98 (0.49), residues: 108 loop : -1.02 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.013 0.002 PHE A 724 TYR 0.014 0.002 TYR A 854 ARG 0.003 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 378) hydrogen bonds : angle 4.48017 ( 1027) metal coordination : bond 0.00301 ( 4) metal coordination : angle 1.30290 ( 3) covalent geometry : bond 0.00306 ( 8512) covalent geometry : angle 0.59593 (11845) *********************** 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 141 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.733 Fit side-chains REVERT: A 666 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6862 (pp20) REVERT: A 734 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7630 (m) REVERT: A 767 GLU cc_start: 0.6396 (tp30) cc_final: 0.5829 (tp30) REVERT: A 788 ILE cc_start: 0.8353 (tp) cc_final: 0.8146 (tp) REVERT: A 953 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7466 (ttt90) REVERT: A 998 GLU cc_start: 0.7987 (tt0) cc_final: 0.7654 (tt0) REVERT: A 1019 ASP cc_start: 0.7596 (t70) cc_final: 0.7219 (t0) REVERT: A 1338 ARG cc_start: 0.6660 (ttp80) cc_final: 0.6133 (ttm-80) REVERT: A 1375 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7727 (pttm) REVERT: A 1417 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 1472 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.1472 (ptm) REVERT: A 1528 ARG cc_start: 0.7541 (mpp80) cc_final: 0.6174 (mmm160) REVERT: A 1532 ARG cc_start: 0.5862 (ttm-80) cc_final: 0.5626 (mtp85) REVERT: A 1564 LYS cc_start: 0.6979 (mmtp) cc_final: 0.6192 (mmmm) outliers start: 41 outliers final: 31 residues processed: 130 average time/residue: 0.2176 time to fit residues: 37.8949 Evaluate side-chains 132 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 1232 ASP 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 1472 MET 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 Chi-restraints excluded: chain A residue 1566 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123422 restraints weight = 10371.017| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.61 r_work: 0.3296 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3135 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= 0.180 Angle : 0.629 9.664 11848 Z= 0.316 Chirality : 0.040 0.241 1399 Planarity : 0.004 0.063 1251 Dihedral : 16.627 74.110 1979 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.54 % Allowed : 18.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 829 helix: 1.14 (0.27), residues: 360 sheet: -0.77 (0.49), residues: 106 loop : -0.94 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.014 0.002 PHE A1203 TYR 0.015 0.002 TYR A1143 ARG 0.003 0.001 ARG A1098 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 378) hydrogen bonds : angle 4.59862 ( 1027) metal coordination : bond 0.00438 ( 4) metal coordination : angle 2.12117 ( 3) covalent geometry : bond 0.00396 ( 8512) covalent geometry : angle 0.62843 (11845) *********************** 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 136 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.255 Fit side-chains REVERT: A 666 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: A 734 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7608 (m) REVERT: A 767 GLU cc_start: 0.6398 (tp30) cc_final: 0.5805 (tp30) REVERT: A 788 ILE cc_start: 0.8372 (tp) cc_final: 0.8160 (tp) REVERT: A 841 GLU cc_start: 0.7117 (pp20) cc_final: 0.6656 (pp20) REVERT: A 953 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7349 (ttt90) REVERT: A 1338 ARG cc_start: 0.6803 (ttp80) cc_final: 0.6235 (ttm-80) REVERT: A 1375 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7569 (pttm) REVERT: A 1417 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 1528 ARG cc_start: 0.7638 (mpp80) cc_final: 0.6241 (mmm160) REVERT: A 1532 ARG cc_start: 0.5844 (ttm-80) cc_final: 0.5632 (mtp85) REVERT: A 1564 LYS cc_start: 0.6944 (mmtp) cc_final: 0.6118 (mmmm) outliers start: 34 outliers final: 28 residues processed: 129 average time/residue: 0.2282 time to fit residues: 40.0689 Evaluate side-chains 126 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 1074 GLU 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 1232 ASP 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 67 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.153695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127519 restraints weight = 10251.263| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.59 r_work: 0.3274 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3263 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= 0.152 Angle : 0.614 10.318 11848 Z= 0.308 Chirality : 0.039 0.234 1399 Planarity : 0.004 0.065 1251 Dihedral : 16.637 74.082 1979 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.94 % Allowed : 18.42 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 829 helix: 1.17 (0.27), residues: 361 sheet: -0.74 (0.49), residues: 106 loop : -0.87 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.013 0.002 PHE A 724 TYR 0.014 0.002 TYR A1220 ARG 0.003 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 378) hydrogen bonds : angle 4.54448 ( 1027) metal coordination : bond 0.00355 ( 4) metal coordination : angle 1.51836 ( 3) covalent geometry : bond 0.00332 ( 8512) covalent geometry : angle 0.61366 (11845) ********************** 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 135 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.985 Fit side-chains REVERT: A 666 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6806 (pp20) REVERT: A 734 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7630 (m) REVERT: A 767 GLU cc_start: 0.6355 (tp30) cc_final: 0.5783 (tp30) REVERT: A 788 ILE cc_start: 0.8360 (tp) cc_final: 0.8153 (tp) REVERT: A 841 GLU cc_start: 0.7061 (pp20) cc_final: 0.6592 (pp20) REVERT: A 953 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7324 (ttt90) REVERT: A 998 GLU cc_start: 0.7987 (tt0) cc_final: 0.7550 (tt0) REVERT: A 1019 ASP cc_start: 0.7652 (t70) cc_final: 0.7250 (t0) REVERT: A 1338 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6214 (ttm-80) REVERT: A 1375 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7521 (pttm) REVERT: A 1417 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6944 (mp) REVERT: A 1528 ARG cc_start: 0.7560 (mpp80) cc_final: 0.6215 (mmm160) REVERT: A 1532 ARG cc_start: 0.5839 (ttm-80) cc_final: 0.5617 (mtp85) REVERT: A 1564 LYS cc_start: 0.6997 (mmtp) cc_final: 0.6186 (mmmm) outliers start: 37 outliers final: 32 residues processed: 127 average time/residue: 0.3532 time to fit residues: 59.9023 Evaluate side-chains 131 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 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 1209 ILE Chi-restraints excluded: chain A residue 1232 ASP 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 Chi-restraints excluded: chain A residue 1566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.0030 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130292 restraints weight = 10380.943| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.56 r_work: 0.3351 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8516 Z= 0.126 Angle : 0.593 10.782 11848 Z= 0.297 Chirality : 0.038 0.223 1399 Planarity : 0.004 0.064 1251 Dihedral : 16.675 74.131 1979 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.67 % Allowed : 18.96 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.30), residues: 829 helix: 1.30 (0.27), residues: 356 sheet: -0.86 (0.49), residues: 108 loop : -0.82 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1125 HIS 0.012 0.001 HIS A1274 PHE 0.012 0.001 PHE A1087 TYR 0.014 0.001 TYR A 854 ARG 0.004 0.000 ARG A1044 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 378) hydrogen bonds : angle 4.49215 ( 1027) metal coordination : bond 0.00354 ( 4) metal coordination : angle 1.03561 ( 3) covalent geometry : bond 0.00268 ( 8512) covalent geometry : angle 0.59261 (11845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5441.11 seconds wall clock time: 98 minutes 49.70 seconds (5929.70 seconds total)