Starting phenix.real_space_refine (version: 1.20rc2) on Mon Nov 1 20:07:10 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_31963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_31963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_31963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_31963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg2_31963/11_2021/7vg2_31963.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 627": "NH1" <-> "NH2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A PHE 1340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1373": "NH1" <-> "NH2" Residue "A ARG 1423": "NH1" <-> "NH2" Residue "A ARG 1478": "NH1" <-> "NH2" Residue "A ASP 1544": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc2-4405/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: {'rna3p_pyr': 16, 'rna2p_pur': 1, 'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 17} Link IDs: {'rna3p': 32, 'rna2p': 2} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 762 Classifications: {'RNA': 36} Modifications used: {'rna3p_pyr': 19, 'rna3p_pur': 17} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1, ' CA': 2} 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: 4.88, per 1000 atoms: 0.59 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 - 3.50 Amimo acid : False - 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: 3.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 2.79 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: 3.60 Time building geometry restraints manager: 3.67 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: 93.52 - 101.70: 122 101.70 - 109.88: 2220 109.88 - 118.06: 4681 118.06 - 126.24: 4503 126.24 - 134.42: 319 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA ASN A1405 " pdb=" CB ASN A1405 " pdb=" CG ASN A1405 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.71e+01 angle pdb=" N PRO A1006 " pdb=" CA PRO A1006 " pdb=" C PRO A1006 " ideal model delta sigma weight residual 110.95 103.02 7.93 1.62e+00 3.81e-01 2.40e+01 angle pdb=" C THR A1404 " pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N GLY A 649 " pdb=" CA GLY A 649 " pdb=" C GLY A 649 " ideal model delta sigma weight residual 111.36 116.80 -5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" C LEU A 763 " pdb=" CA LEU A 763 " pdb=" CB LEU A 763 " ideal model delta sigma weight residual 109.75 117.22 -7.47 1.65e+00 3.67e-01 2.05e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 4504 15.87 - 31.74: 362 31.74 - 47.61: 94 47.61 - 63.47: 28 63.47 - 79.34: 5 Dihedral angle restraints: 4993 sinusoidal: 2528 harmonic: 2465 Sorted by residual: dihedral pdb=" CA PHE A1164 " pdb=" C PHE A1164 " pdb=" N ASP A1165 " pdb=" CA ASP A1165 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASP A1165 " pdb=" C ASP A1165 " pdb=" N PRO A1166 " pdb=" CA PRO A1166 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY A1310 " pdb=" C GLY A1310 " pdb=" N PRO A1311 " pdb=" CA PRO A1311 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 4990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1097 0.096 - 0.191: 260 0.191 - 0.287: 30 0.287 - 0.382: 7 0.382 - 0.478: 5 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU A1556 " pdb=" CB LEU A1556 " pdb=" CD1 LEU A1556 " pdb=" CD2 LEU A1556 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CB VAL A1374 " pdb=" CA VAL A1374 " pdb=" CG1 VAL A1374 " pdb=" CG2 VAL A1374 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA LEU A 763 " pdb=" N LEU A 763 " pdb=" C LEU A 763 " pdb=" CB LEU A 763 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1396 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " -0.042 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR A1142 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 19 " -0.047 2.00e-02 2.50e+03 3.03e-02 2.07e+01 pdb=" N1 U C 19 " 0.075 2.00e-02 2.50e+03 pdb=" C2 U C 19 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C 19 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 19 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U C 19 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U C 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U C 19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1243 " -0.043 2.00e-02 2.50e+03 3.02e-02 1.82e+01 pdb=" CG TYR A1243 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A1243 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A1243 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A1243 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1243 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A1243 " -0.005 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 38 2.44 - 3.05: 5021 3.05 - 3.67: 14133 3.67 - 4.28: 21155 4.28 - 4.90: 32202 Nonbonded interactions: 72549 Sorted by model distance: nonbonded pdb=" OD1 ASP A1316 " pdb="CA CA A2002 " model vdw 1.822 2.660 nonbonded pdb=" OE1 GLU A1136 " pdb="CA CA A2001 " model vdw 2.072 2.660 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 2.660 ... (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 ========== 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 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. 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 Write .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: 0.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.870 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 28.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.530 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 12.864 79.342 3389 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.96 % Favored : 91.80 % Rotamer Outliers : 1.74 % 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.965 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 142 average time/residue: 0.2362 time to fit residues: 44.4999 Evaluate side-chains 100 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0892 time to fit residues: 2.2589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A1197 HIS A1241 ASN ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN A1488 HIS A1569 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2311 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= 0.217 Angle : 0.647 9.371 11845 Z= 0.330 Chirality : 0.039 0.175 1399 Planarity : 0.005 0.053 1251 Dihedral : 8.395 59.354 1749 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer Outliers : 2.67 % 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: -1.90 (0.27), residues: 829 helix: -0.43 (0.24), residues: 358 sheet: -1.84 (0.44), residues: 129 loop : -1.81 (0.31), residues: 342 *********************** 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 145 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.870 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.2222 time to fit residues: 41.7339 Evaluate side-chains 113 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0790 time to fit residues: 2.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 GLN A1488 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8512 Z= 0.201 Angle : 0.600 9.648 11845 Z= 0.303 Chirality : 0.037 0.146 1399 Planarity : 0.004 0.054 1251 Dihedral : 7.840 55.876 1749 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.15 % Favored : 93.73 % Rotamer Outliers : 2.40 % 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: -0.94 (0.28), residues: 829 helix: 0.61 (0.26), residues: 357 sheet: -1.66 (0.45), residues: 129 loop : -1.47 (0.33), residues: 343 *********************** 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 127 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.831 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 123 average time/residue: 0.2327 time to fit residues: 38.2288 Evaluate side-chains 105 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0845 time to fit residues: 2.8767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0040 chunk 42 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 967 HIS A 977 GLN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8512 Z= 0.160 Angle : 0.565 9.864 11845 Z= 0.281 Chirality : 0.036 0.187 1399 Planarity : 0.004 0.050 1251 Dihedral : 7.541 58.496 1749 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer Outliers : 2.40 % 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: 1.20 (0.27), residues: 357 sheet: -1.52 (0.45), residues: 128 loop : -1.23 (0.33), residues: 344 *********************** 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 123 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.845 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 115 average time/residue: 0.2306 time to fit residues: 35.5285 Evaluate side-chains 100 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0748 time to fit residues: 2.4964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 GLN A1211 HIS A1274 HIS ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1488 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.050 8512 Z= 0.271 Angle : 0.631 9.400 11845 Z= 0.317 Chirality : 0.040 0.309 1399 Planarity : 0.004 0.058 1251 Dihedral : 7.826 58.629 1749 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.00 % Favored : 92.88 % Rotamer Outliers : 2.14 % 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: 1.13 (0.27), residues: 357 sheet: -1.31 (0.45), residues: 128 loop : -1.10 (0.34), residues: 344 *********************** 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 121 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.815 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 118 average time/residue: 0.2344 time to fit residues: 37.3193 Evaluate side-chains 106 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0875 time to fit residues: 2.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 GLN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1274 HIS A1278 GLN A1488 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 8512 Z= 0.199 Angle : 0.595 8.903 11845 Z= 0.300 Chirality : 0.037 0.262 1399 Planarity : 0.004 0.076 1251 Dihedral : 7.643 56.722 1749 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer Outliers : 1.74 % 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: -0.16 (0.29), residues: 829 helix: 1.19 (0.27), residues: 363 sheet: -1.27 (0.45), residues: 128 loop : -1.00 (0.35), residues: 338 *********************** 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 108 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.918 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.2505 time to fit residues: 34.0855 Evaluate side-chains 95 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0801 time to fit residues: 2.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 8512 Z= 0.212 Angle : 0.579 8.954 11845 Z= 0.292 Chirality : 0.037 0.238 1399 Planarity : 0.005 0.114 1251 Dihedral : 7.440 56.932 1749 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer Outliers : 1.07 % 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: -0.01 (0.30), residues: 829 helix: 1.32 (0.27), residues: 362 sheet: -1.21 (0.45), residues: 128 loop : -0.91 (0.35), residues: 339 *********************** 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 103 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.009 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.2355 time to fit residues: 32.0167 Evaluate side-chains 88 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0903 time to fit residues: 1.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 GLN A1274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.114 8512 Z= 0.211 Angle : 0.584 9.418 11845 Z= 0.297 Chirality : 0.037 0.218 1399 Planarity : 0.005 0.112 1251 Dihedral : 7.366 56.745 1749 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Rotamer Outliers : 1.47 % 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: 0.05 (0.30), residues: 829 helix: 1.44 (0.27), residues: 357 sheet: -1.11 (0.45), residues: 128 loop : -0.97 (0.35), residues: 344 *********************** 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 105 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.852 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.2354 time to fit residues: 32.2128 Evaluate side-chains 94 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0893 time to fit residues: 2.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 GLN A1274 HIS A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 8512 Z= 0.275 Angle : 0.622 9.449 11845 Z= 0.315 Chirality : 0.039 0.254 1399 Planarity : 0.005 0.123 1251 Dihedral : 7.453 59.943 1749 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.24 (0.27), residues: 360 sheet: -1.09 (0.44), residues: 128 loop : -0.87 (0.35), residues: 341 *********************** 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 98 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.802 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2111 time to fit residues: 27.6022 Evaluate side-chains 92 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0954 time to fit residues: 1.9760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 8512 Z= 0.212 Angle : 0.589 9.981 11845 Z= 0.297 Chirality : 0.037 0.239 1399 Planarity : 0.005 0.112 1251 Dihedral : 7.300 56.796 1749 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.27 (0.27), residues: 361 sheet: -1.01 (0.45), residues: 128 loop : -0.88 (0.35), residues: 340 ********************** 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 95 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.880 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.2382 time to fit residues: 30.3661 Evaluate side-chains 90 residues out of total 749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0817 time to fit residues: 1.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0050 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131981 restraints weight = 10404.767| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.58 r_work: 0.3471 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.3438 rms_B_bonded: 1.63 restraints_weight: 0.1250 r_work: 0.3415 rms_B_bonded: 1.90 restraints_weight: 0.0625 r_work: 0.3387 rms_B_bonded: 2.31 restraints_weight: 0.0312 r_work: 0.3351 rms_B_bonded: 2.90 restraints_weight: 0.0156 r_work: 0.3303 rms_B_bonded: 3.76 restraints_weight: 0.0078 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.207 8512 Z= 0.267 Angle : 0.619 14.798 11845 Z= 0.323 Chirality : 0.037 0.227 1399 Planarity : 0.005 0.137 1251 Dihedral : 7.205 56.310 1749 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.00 (0.30), residues: 829 helix: 1.23 (0.27), residues: 365 sheet: -0.98 (0.44), residues: 128 loop : -0.91 (0.35), residues: 336 =============================================================================== Job complete usr+sys time: 1644.48 seconds wall clock time: 30 minutes 51.51 seconds (1851.51 seconds total)