Starting phenix.real_space_refine on Wed Feb 12 21:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vg2_31963/02_2025/7vg2_31963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vg2_31963/02_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_31963/02_2025/7vg2_31963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vg2_31963/02_2025/7vg2_31963.map" model { file = "/net/cci-nas-00/data/ceres_data/7vg2_31963/02_2025/7vg2_31963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vg2_31963/02_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-5592/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: 5.25, per 1000 atoms: 0.64 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: 2.41 Conformation dependent library (CDL) restraints added in 842.3 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: 3.16 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: 3.48 Time building geometry restraints manager: 2.67 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: 0.270 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.660 Find NCS groups from input model: 0.080 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- 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 8512 Z= 1.044 Angle : 1.432 10.314 11845 Z= 0.815 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 *********************** 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 : 0.726 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: 0.2470 time to fit residues: 45.9868 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 : 0.889 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123276 restraints weight = 10208.932| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.66 r_work: 0.3218 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 8512 Z= 0.227 Angle : 0.684 9.286 11845 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 *********************** 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 : 0.807 Fit side-chains REVERT: A 734 VAL cc_start: 0.8030 (p) cc_final: 0.7310 (m) REVERT: A 756 HIS cc_start: 0.8188 (m90) cc_final: 0.7982 (m-70) REVERT: A 841 GLU cc_start: 0.6887 (pp20) cc_final: 0.6350 (pp20) REVERT: A 1019 ASP cc_start: 0.7736 (t0) cc_final: 0.7180 (t70) REVERT: A 1038 ASP cc_start: 0.8237 (p0) cc_final: 0.7965 (p0) REVERT: A 1085 SER cc_start: 0.8709 (m) cc_final: 0.8366 (p) REVERT: A 1145 SER cc_start: 0.8268 (m) cc_final: 0.8026 (m) REVERT: A 1202 LYS cc_start: 0.7820 (mttp) cc_final: 0.7343 (mmtt) REVERT: A 1338 ARG cc_start: 0.6740 (ttp80) cc_final: 0.6200 (ttm-80) REVERT: A 1528 ARG cc_start: 0.7676 (mpp80) cc_final: 0.6411 (mmm160) outliers start: 26 outliers final: 15 residues processed: 140 average time/residue: 0.2076 time to fit residues: 40.0280 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 : 0.817 ------------------------------------------------------------------------------- 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: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** 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 = 0.3624 r_free = 0.3624 target = 0.147600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120307 restraints weight = 10432.116| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.66 r_work: 0.3179 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8512 Z= 0.269 Angle : 0.663 9.712 11845 Z= 0.339 Chirality : 0.040 0.272 1399 Planarity : 0.005 0.057 1251 Dihedral : 17.023 74.026 1982 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.66 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: -1.21 (0.28), residues: 829 helix: 0.21 (0.25), residues: 353 sheet: -1.57 (0.46), residues: 127 loop : -1.48 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1125 HIS 0.005 0.001 HIS A1276 PHE 0.017 0.002 PHE A1203 TYR 0.017 0.002 TYR A1142 ARG 0.005 0.001 ARG A1222 *********************** 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 138 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.832 Fit side-chains REVERT: A 734 VAL cc_start: 0.8138 (p) cc_final: 0.7527 (m) REVERT: A 830 PHE cc_start: 0.8669 (m-80) cc_final: 0.8466 (m-80) REVERT: A 841 GLU cc_start: 0.6943 (pp20) cc_final: 0.6345 (pp20) REVERT: A 1003 LEU cc_start: 0.8990 (tp) cc_final: 0.8778 (mt) REVERT: A 1019 ASP cc_start: 0.7651 (t70) cc_final: 0.7157 (t70) REVERT: A 1085 SER cc_start: 0.8813 (m) cc_final: 0.8450 (p) REVERT: A 1164 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.5939 (t80) REVERT: A 1224 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: A 1338 ARG cc_start: 0.6705 (ttp80) cc_final: 0.6194 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7077 (mp) REVERT: A 1528 ARG cc_start: 0.7614 (mpp80) cc_final: 0.6232 (mmm160) outliers start: 34 outliers final: 23 residues processed: 128 average time/residue: 0.2241 time to fit residues: 39.1257 Evaluate side-chains 120 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.153877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127571 restraints weight = 10243.158| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.61 r_work: 0.3265 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.032 8512 Z= 0.191 Angle : 0.606 10.611 11845 Z= 0.306 Chirality : 0.038 0.196 1399 Planarity : 0.004 0.051 1251 Dihedral : 16.973 73.960 1981 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 4.67 % Allowed : 14.42 % Favored : 80.91 % 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: -0.62 (0.29), residues: 829 helix: 0.71 (0.26), residues: 363 sheet: -1.18 (0.49), residues: 108 loop : -1.28 (0.32), residues: 358 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 A1220 ARG 0.004 0.000 ARG A1515 *********************** 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 135 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.807 Fit side-chains REVERT: A 734 VAL cc_start: 0.8128 (p) cc_final: 0.7568 (m) REVERT: A 841 GLU cc_start: 0.7041 (pp20) cc_final: 0.6415 (pp20) REVERT: A 1085 SER cc_start: 0.8802 (m) cc_final: 0.8451 (p) REVERT: A 1164 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5934 (t80) REVERT: A 1202 LYS cc_start: 0.7725 (mttp) cc_final: 0.7402 (mmtt) REVERT: A 1224 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: A 1276 HIS cc_start: 0.7960 (m-70) cc_final: 0.7746 (m-70) REVERT: A 1338 ARG cc_start: 0.6548 (ttp80) cc_final: 0.6041 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6954 (mp) REVERT: A 1528 ARG cc_start: 0.7437 (mpp80) cc_final: 0.6094 (mmm160) outliers start: 35 outliers final: 24 residues processed: 125 average time/residue: 0.2160 time to fit residues: 36.5696 Evaluate side-chains 124 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 1224 GLU 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 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: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 0.0040 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.156074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131191 restraints weight = 10165.890| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.53 r_work: 0.3314 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8512 Z= 0.180 Angle : 0.587 10.937 11845 Z= 0.295 Chirality : 0.037 0.175 1399 Planarity : 0.004 0.049 1251 Dihedral : 16.836 74.071 1979 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 4.94 % Allowed : 15.75 % Favored : 79.31 % 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: -0.38 (0.29), residues: 829 helix: 1.09 (0.27), residues: 358 sheet: -1.52 (0.45), residues: 129 loop : -1.12 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1125 HIS 0.010 0.001 HIS A1274 PHE 0.013 0.001 PHE A1203 TYR 0.014 0.001 TYR A 854 ARG 0.004 0.000 ARG A1515 *********************** 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 145 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.762 Fit side-chains REVERT: A 734 VAL cc_start: 0.8122 (p) cc_final: 0.7617 (m) REVERT: A 767 GLU cc_start: 0.6302 (tp30) cc_final: 0.5922 (tp30) REVERT: A 788 ILE cc_start: 0.8347 (tp) cc_final: 0.8126 (tp) REVERT: A 841 GLU cc_start: 0.7026 (pp20) cc_final: 0.6475 (pp20) REVERT: A 998 GLU cc_start: 0.7967 (tt0) cc_final: 0.7631 (tt0) REVERT: A 1019 ASP cc_start: 0.7605 (t70) cc_final: 0.7172 (t0) REVERT: A 1085 SER cc_start: 0.8774 (m) cc_final: 0.8423 (p) REVERT: A 1120 ASP cc_start: 0.7848 (m-30) cc_final: 0.7443 (m-30) REVERT: A 1202 LYS cc_start: 0.7715 (mttp) cc_final: 0.7502 (mmtt) REVERT: A 1338 ARG cc_start: 0.6449 (ttp80) cc_final: 0.5992 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6762 (mp) REVERT: A 1528 ARG cc_start: 0.7407 (mpp80) cc_final: 0.6141 (mmm160) REVERT: A 1564 LYS cc_start: 0.6897 (mmtp) cc_final: 0.6159 (mmmm) outliers start: 37 outliers final: 27 residues processed: 135 average time/residue: 0.2440 time to fit residues: 43.9448 Evaluate side-chains 124 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.152604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126459 restraints weight = 10273.868| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.59 r_work: 0.3287 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8512 Z= 0.226 Angle : 0.611 9.924 11845 Z= 0.308 Chirality : 0.038 0.182 1399 Planarity : 0.004 0.052 1251 Dihedral : 16.740 74.094 1979 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 5.07 % Allowed : 17.36 % 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: -0.22 (0.29), residues: 829 helix: 1.04 (0.27), residues: 364 sheet: -0.99 (0.48), residues: 106 loop : -1.06 (0.33), residues: 359 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 0.002 TYR A 854 ARG 0.004 0.000 ARG A1515 *********************** 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 144 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.685 Fit side-chains REVERT: A 666 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: A 734 VAL cc_start: 0.8139 (p) cc_final: 0.7626 (m) REVERT: A 767 GLU cc_start: 0.6469 (tp30) cc_final: 0.6096 (tp30) REVERT: A 788 ILE cc_start: 0.8349 (tp) cc_final: 0.8142 (tp) REVERT: A 953 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7484 (ttt90) REVERT: A 998 GLU cc_start: 0.7990 (tt0) cc_final: 0.7649 (tt0) REVERT: A 1019 ASP cc_start: 0.7641 (t70) cc_final: 0.7246 (t70) REVERT: A 1202 LYS cc_start: 0.7779 (mttp) cc_final: 0.7469 (mmtt) REVERT: A 1338 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6169 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6939 (mp) REVERT: A 1472 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.1397 (ptm) REVERT: A 1528 ARG cc_start: 0.7511 (mpp80) cc_final: 0.6185 (mmm160) REVERT: A 1564 LYS cc_start: 0.6926 (mmtp) cc_final: 0.6156 (mmmm) outliers start: 38 outliers final: 27 residues processed: 136 average time/residue: 0.2502 time to fit residues: 44.6690 Evaluate side-chains 128 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.153763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127622 restraints weight = 10273.543| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.60 r_work: 0.3313 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8512 Z= 0.191 Angle : 0.596 10.375 11845 Z= 0.299 Chirality : 0.038 0.246 1399 Planarity : 0.004 0.050 1251 Dihedral : 16.743 74.114 1979 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 5.74 % Allowed : 16.42 % 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: -0.11 (0.29), residues: 829 helix: 1.22 (0.27), residues: 359 sheet: -1.06 (0.48), residues: 108 loop : -1.04 (0.33), residues: 362 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 A1203 TYR 0.014 0.001 TYR A 854 ARG 0.003 0.000 ARG A1532 *********************** 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 144 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.781 Fit side-chains REVERT: A 666 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: A 734 VAL cc_start: 0.8113 (p) cc_final: 0.7596 (m) REVERT: A 767 GLU cc_start: 0.6389 (tp30) cc_final: 0.5995 (tp30) REVERT: A 788 ILE cc_start: 0.8345 (tp) cc_final: 0.8133 (tp) REVERT: A 953 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7490 (ttt90) REVERT: A 998 GLU cc_start: 0.8027 (tt0) cc_final: 0.7686 (tt0) REVERT: A 1019 ASP cc_start: 0.7643 (t70) cc_final: 0.7194 (t70) REVERT: A 1202 LYS cc_start: 0.7673 (mttp) cc_final: 0.7468 (mmtt) REVERT: A 1338 ARG cc_start: 0.6748 (ttp80) cc_final: 0.6159 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6928 (mp) REVERT: A 1472 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.1398 (ptm) REVERT: A 1528 ARG cc_start: 0.7498 (mpp80) cc_final: 0.6163 (mmm160) REVERT: A 1564 LYS cc_start: 0.6979 (mmtp) cc_final: 0.6167 (mmmm) outliers start: 43 outliers final: 31 residues processed: 134 average time/residue: 0.2431 time to fit residues: 43.1661 Evaluate side-chains 129 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.150459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125292 restraints weight = 10318.465| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.62 r_work: 0.3289 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8512 Z= 0.240 Angle : 0.621 10.045 11845 Z= 0.312 Chirality : 0.039 0.232 1399 Planarity : 0.004 0.052 1251 Dihedral : 16.658 74.102 1979 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 5.61 % Allowed : 16.56 % 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: -0.03 (0.29), residues: 829 helix: 1.18 (0.27), residues: 360 sheet: -0.84 (0.49), residues: 106 loop : -0.95 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1125 HIS 0.011 0.001 HIS A1274 PHE 0.014 0.002 PHE A 724 TYR 0.015 0.002 TYR A1143 ARG 0.003 0.000 ARG A1098 *********************** 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 146 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.860 Fit side-chains REVERT: A 666 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: A 734 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7635 (m) REVERT: A 767 GLU cc_start: 0.6300 (tp30) cc_final: 0.5902 (tp30) REVERT: A 788 ILE cc_start: 0.8367 (tp) cc_final: 0.8150 (tp) REVERT: A 953 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7417 (ttt90) REVERT: A 998 GLU cc_start: 0.7984 (tt0) cc_final: 0.7654 (tt0) REVERT: A 1019 ASP cc_start: 0.7708 (t70) cc_final: 0.7325 (t70) REVERT: A 1202 LYS cc_start: 0.7854 (mttp) cc_final: 0.7579 (mmtt) REVERT: A 1338 ARG cc_start: 0.6735 (ttp80) cc_final: 0.6201 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7051 (mp) REVERT: A 1472 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5538 (mmm) REVERT: A 1528 ARG cc_start: 0.7516 (mpp80) cc_final: 0.6226 (mmm160) REVERT: A 1564 LYS cc_start: 0.6963 (mmtp) cc_final: 0.6186 (mmmm) outliers start: 42 outliers final: 35 residues processed: 136 average time/residue: 0.2416 time to fit residues: 43.4825 Evaluate side-chains 138 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 1113 ILE 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 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: 0.0030 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.154309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128466 restraints weight = 10389.415| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.59 r_work: 0.3321 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8512 Z= 0.195 Angle : 0.604 10.657 11845 Z= 0.303 Chirality : 0.038 0.215 1399 Planarity : 0.004 0.049 1251 Dihedral : 16.687 74.085 1979 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.34 % Allowed : 17.76 % Favored : 76.90 % 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: 0.02 (0.30), residues: 829 helix: 1.29 (0.27), residues: 358 sheet: -0.93 (0.49), residues: 108 loop : -0.96 (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 0.012 0.001 PHE A1203 TYR 0.013 0.002 TYR A 854 ARG 0.004 0.000 ARG A1532 *********************** 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 143 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.764 Fit side-chains REVERT: A 666 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6900 (pp20) REVERT: A 734 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7616 (m) REVERT: A 767 GLU cc_start: 0.6231 (tp30) cc_final: 0.5821 (tp30) REVERT: A 788 ILE cc_start: 0.8376 (tp) cc_final: 0.8146 (tp) REVERT: A 953 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7405 (ttt90) REVERT: A 998 GLU cc_start: 0.7968 (tt0) cc_final: 0.7628 (tt0) REVERT: A 1019 ASP cc_start: 0.7709 (t70) cc_final: 0.7228 (t0) REVERT: A 1202 LYS cc_start: 0.7710 (mttp) cc_final: 0.7489 (mmtt) REVERT: A 1253 ASP cc_start: 0.8122 (m-30) cc_final: 0.7893 (m-30) REVERT: A 1338 ARG cc_start: 0.6689 (ttp80) cc_final: 0.6162 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6856 (mp) REVERT: A 1472 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.1403 (ptm) REVERT: A 1528 ARG cc_start: 0.7420 (mpp80) cc_final: 0.6157 (mmm160) REVERT: A 1564 LYS cc_start: 0.6990 (mmtp) cc_final: 0.6186 (mmmm) outliers start: 40 outliers final: 31 residues processed: 132 average time/residue: 0.2428 time to fit residues: 42.3807 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 : 0.760 ------------------------------------------------------------------------------- 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 1176 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** A1278 GLN A1384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131117 restraints weight = 10236.408| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.56 r_work: 0.3359 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8512 Z= 0.186 Angle : 0.597 10.840 11845 Z= 0.299 Chirality : 0.038 0.207 1399 Planarity : 0.004 0.061 1251 Dihedral : 16.665 74.107 1979 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.81 % Allowed : 18.69 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.29), residues: 829 helix: 1.31 (0.27), residues: 355 sheet: -0.91 (0.48), residues: 108 loop : -0.90 (0.33), residues: 366 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 0.001 PHE A 724 TYR 0.013 0.001 TYR A 854 ARG 0.004 0.000 ARG A1532 ********************** 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 138 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.771 Fit side-chains REVERT: A 666 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6872 (pp20) REVERT: A 734 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7623 (m) REVERT: A 767 GLU cc_start: 0.6215 (tp30) cc_final: 0.5792 (tp30) REVERT: A 788 ILE cc_start: 0.8386 (tp) cc_final: 0.8166 (tp) REVERT: A 953 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7431 (ttt90) REVERT: A 998 GLU cc_start: 0.7949 (tt0) cc_final: 0.7600 (tt0) REVERT: A 1019 ASP cc_start: 0.7666 (t70) cc_final: 0.7205 (t0) REVERT: A 1120 ASP cc_start: 0.7872 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1202 LYS cc_start: 0.7633 (mttp) cc_final: 0.7391 (mmtt) REVERT: A 1253 ASP cc_start: 0.8127 (m-30) cc_final: 0.7883 (m-30) REVERT: A 1338 ARG cc_start: 0.6680 (ttp80) cc_final: 0.6151 (ttm-80) REVERT: A 1417 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 1472 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.1758 (ptm) REVERT: A 1528 ARG cc_start: 0.7432 (mpp80) cc_final: 0.6181 (mmm160) REVERT: A 1564 LYS cc_start: 0.7007 (mmtp) cc_final: 0.6224 (mmmm) outliers start: 36 outliers final: 30 residues processed: 129 average time/residue: 0.2404 time to fit residues: 41.2478 Evaluate side-chains 132 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 1176 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.157710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132271 restraints weight = 10384.762| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.59 r_work: 0.3372 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8512 Z= 0.167 Angle : 0.583 11.137 11845 Z= 0.290 Chirality : 0.037 0.206 1399 Planarity : 0.004 0.062 1251 Dihedral : 16.683 74.136 1979 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.81 % Allowed : 18.42 % 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: 0.14 (0.30), residues: 829 helix: 1.38 (0.27), residues: 355 sheet: -0.87 (0.49), residues: 108 loop : -0.85 (0.33), residues: 366 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 A1233 TYR 0.016 0.001 TYR A1143 ARG 0.006 0.000 ARG A1532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4834.70 seconds wall clock time: 86 minutes 21.76 seconds (5181.76 seconds total)