Starting phenix.real_space_refine on Wed Feb 14 00:10:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/02_2024/8gv8_34287_updated.pdb" } resolution = 3.08 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= 0.002 sd= 0.179 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5422 2.51 5 N 1334 2.21 5 O 1351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8161 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4057 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4048 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 28, 'TRANS': 484} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'4KU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'4KU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.58 Number of scatterers: 8161 At special positions: 0 Unit cell: (86.9, 133.1, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1351 8.00 N 1334 7.00 C 5422 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 Amino 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 0 sheets defined 58.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.695A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.678A pdb=" N VAL A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 818 removed outlier: 3.655A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 846 removed outlier: 4.190A pdb=" N GLU A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 923 removed outlier: 3.503A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 Processing helix chain 'A' and resid 939 through 953 Processing helix chain 'A' and resid 991 through 1019 removed outlier: 3.702A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1039 through 1048 removed outlier: 3.502A pdb=" N GLY A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A1044 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU A1048 " --> pdb=" O GLY A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1092 through 1101 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1115 through 1130 removed outlier: 3.844A pdb=" N GLY A1120 " --> pdb=" O ALA A1116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1130 " --> pdb=" O GLY A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1142 removed outlier: 3.600A pdb=" N LEU A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1153 through 1156 No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'A' and resid 1160 through 1181 removed outlier: 3.537A pdb=" N HIS A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.708A pdb=" N THR A1196 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Proline residue: A1198 - end of helix removed outlier: 4.289A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A1207 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1216 Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 706 through 733 removed outlier: 3.692A pdb=" N ALA B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 740 through 757 removed outlier: 3.712A pdb=" N LEU B 749 " --> pdb=" O MET B 745 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 789 through 809 removed outlier: 3.677A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 796 " --> pdb=" O GLY B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.739A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 833 No H-bonds generated for 'chain 'B' and resid 830 through 833' Processing helix chain 'B' and resid 900 through 923 removed outlier: 3.702A pdb=" N PHE B 916 " --> pdb=" O PHE B 912 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 917 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 920 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 937 Processing helix chain 'B' and resid 939 through 953 Processing helix chain 'B' and resid 991 through 1019 removed outlier: 3.696A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Proline residue: B1000 - end of helix Processing helix chain 'B' and resid 1036 through 1048 removed outlier: 3.826A pdb=" N LEU B1048 " --> pdb=" O GLY B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 Processing helix chain 'B' and resid 1092 through 1104 removed outlier: 4.914A pdb=" N ILE B1104 " --> pdb=" O VAL B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1115 through 1130 removed outlier: 3.872A pdb=" N GLY B1120 " --> pdb=" O ALA B1116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B1130 " --> pdb=" O GLY B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1143 removed outlier: 3.598A pdb=" N LEU B1142 " --> pdb=" O ARG B1138 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B1143 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1148 No H-bonds generated for 'chain 'B' and resid 1146 through 1148' Processing helix chain 'B' and resid 1153 through 1156 No H-bonds generated for 'chain 'B' and resid 1153 through 1156' Processing helix chain 'B' and resid 1160 through 1181 removed outlier: 3.549A pdb=" N HIS B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B1166 " --> pdb=" O ARG B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1207 removed outlier: 3.708A pdb=" N THR B1196 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Proline residue: B1198 - end of helix removed outlier: 4.287A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B1206 " --> pdb=" O VAL B1202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B1207 " --> pdb=" O VAL B1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1216 345 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 93 1.17 - 1.33: 1783 1.33 - 1.50: 3074 1.50 - 1.67: 3329 1.67 - 1.83: 86 Bond restraints: 8365 Sorted by residual: bond pdb=" C ILE B 836 " pdb=" O ILE B 836 " ideal model delta sigma weight residual 1.241 1.015 0.226 1.03e-02 9.43e+03 4.80e+02 bond pdb=" C LEU B 843 " pdb=" O LEU B 843 " ideal model delta sigma weight residual 1.234 1.000 0.235 1.17e-02 7.31e+03 4.03e+02 bond pdb=" C ILE B 834 " pdb=" O ILE B 834 " ideal model delta sigma weight residual 1.238 1.024 0.214 1.18e-02 7.18e+03 3.30e+02 bond pdb=" C ILE A 836 " pdb=" O ILE A 836 " ideal model delta sigma weight residual 1.241 1.054 0.187 1.03e-02 9.43e+03 3.29e+02 bond pdb=" C TYR B 837 " pdb=" O TYR B 837 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.22e-02 6.72e+03 2.72e+02 ... (remaining 8360 not shown) Histogram of bond angle deviations from ideal: 70.50 - 83.69: 2 83.69 - 96.89: 17 96.89 - 110.09: 1418 110.09 - 123.29: 9486 123.29 - 136.48: 437 Bond angle restraints: 11360 Sorted by residual: angle pdb=" C ASP A1217 " pdb=" CA ASP A1217 " pdb=" CB ASP A1217 " ideal model delta sigma weight residual 111.31 70.50 40.81 1.68e+00 3.54e-01 5.90e+02 angle pdb=" O ILE B 914 " pdb=" C ILE B 914 " pdb=" N ALA B 915 " ideal model delta sigma weight residual 122.57 102.86 19.71 1.25e+00 6.40e-01 2.49e+02 angle pdb=" C PHE B 840 " pdb=" CA PHE B 840 " pdb=" CB PHE B 840 " ideal model delta sigma weight residual 110.42 81.24 29.18 1.99e+00 2.53e-01 2.15e+02 angle pdb=" C GLN A 824 " pdb=" CA GLN A 824 " pdb=" CB GLN A 824 " ideal model delta sigma weight residual 109.75 85.11 24.64 1.72e+00 3.38e-01 2.05e+02 angle pdb=" N LEU A1037 " pdb=" CA LEU A1037 " pdb=" C LEU A1037 " ideal model delta sigma weight residual 114.31 97.28 17.03 1.29e+00 6.01e-01 1.74e+02 ... (remaining 11355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4405 17.71 - 35.42: 403 35.42 - 53.13: 94 53.13 - 70.84: 21 70.84 - 88.55: 8 Dihedral angle restraints: 4931 sinusoidal: 1972 harmonic: 2959 Sorted by residual: dihedral pdb=" C ASP A1217 " pdb=" N ASP A1217 " pdb=" CA ASP A1217 " pdb=" CB ASP A1217 " ideal model delta harmonic sigma weight residual -122.60 -76.87 -45.73 0 2.50e+00 1.60e-01 3.35e+02 dihedral pdb=" C PHE B 840 " pdb=" N PHE B 840 " pdb=" CA PHE B 840 " pdb=" CB PHE B 840 " ideal model delta harmonic sigma weight residual -122.60 -88.67 -33.93 0 2.50e+00 1.60e-01 1.84e+02 dihedral pdb=" C GLN A 824 " pdb=" N GLN A 824 " pdb=" CA GLN A 824 " pdb=" CB GLN A 824 " ideal model delta harmonic sigma weight residual -122.60 -92.85 -29.75 0 2.50e+00 1.60e-01 1.42e+02 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1231 0.145 - 0.290: 68 0.290 - 0.434: 23 0.434 - 0.579: 9 0.579 - 0.724: 4 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 752 " pdb=" CA VAL A 752 " pdb=" CG1 VAL A 752 " pdb=" CG2 VAL A 752 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR A 841 " pdb=" N TYR A 841 " pdb=" C TYR A 841 " pdb=" CB TYR A 841 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU A 838 " pdb=" N GLU A 838 " pdb=" C GLU A 838 " pdb=" CB GLU A 838 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1332 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 914 " 0.046 2.00e-02 2.50e+03 7.85e-02 6.16e+01 pdb=" C ILE B 914 " -0.136 2.00e-02 2.50e+03 pdb=" O ILE B 914 " 0.043 2.00e-02 2.50e+03 pdb=" N ALA B 915 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 838 " 0.034 2.00e-02 2.50e+03 7.12e-02 5.07e+01 pdb=" C GLU B 838 " -0.123 2.00e-02 2.50e+03 pdb=" O GLU B 838 " 0.046 2.00e-02 2.50e+03 pdb=" N THR B 839 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 825 " 0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C GLU A 825 " -0.111 2.00e-02 2.50e+03 pdb=" O GLU A 825 " 0.040 2.00e-02 2.50e+03 pdb=" N ILE A 826 " 0.039 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 3358 2.93 - 3.59: 11063 3.59 - 4.24: 17034 4.24 - 4.90: 30668 Nonbonded interactions: 62132 Sorted by model distance: nonbonded pdb=" O PHE B 840 " pdb=" CB PHE B 840 " model vdw 1.614 2.752 nonbonded pdb=" O ASP A1217 " pdb=" CB ASP A1217 " model vdw 1.635 2.752 nonbonded pdb=" O GLN A 824 " pdb=" CB GLN A 824 " model vdw 2.077 2.752 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.191 2.440 nonbonded pdb=" O GLN B 824 " pdb=" CB GLN B 824 " model vdw 2.238 2.752 ... (remaining 62127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 673 through 855 or resid 894 through 1223 or resid 1501)) selection = chain 'B' } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.980 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.040 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.019 0.235 8365 Z= 1.186 Angle : 1.928 40.813 11360 Z= 1.269 Chirality : 0.094 0.724 1335 Planarity : 0.010 0.098 1390 Dihedral : 14.992 88.551 3017 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.59 % Favored : 93.72 % Rotamer: Outliers : 3.97 % Allowed : 3.63 % Favored : 92.40 % Cbeta Deviations : 5.33 % 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: -0.32 (0.28), residues: 1019 helix: 0.62 (0.23), residues: 636 sheet: None (None), residues: 0 loop : -1.63 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.016 0.001 HIS A 850 PHE 0.040 0.003 PHE B 912 TYR 0.028 0.002 TYR B 837 ARG 0.004 0.000 ARG B1200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8841 (t) REVERT: A 838 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: A 842 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: A 935 ILE cc_start: 0.8158 (mt) cc_final: 0.7885 (mm) REVERT: A 947 MET cc_start: 0.8339 (mmt) cc_final: 0.7884 (mmt) REVERT: A 993 MET cc_start: 0.7368 (tpt) cc_final: 0.6611 (tpt) REVERT: A 1080 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7376 (mptt) REVERT: A 1082 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7357 (ptmm) REVERT: B 817 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (ttp-170) REVERT: B 916 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 925 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7288 (mtm180) REVERT: B 935 ILE cc_start: 0.8159 (mt) cc_final: 0.7884 (mm) REVERT: B 993 MET cc_start: 0.7265 (tpt) cc_final: 0.6521 (tpt) REVERT: B 1075 VAL cc_start: 0.5532 (OUTLIER) cc_final: 0.5223 (t) REVERT: B 1080 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7488 (mppt) REVERT: B 1082 LYS cc_start: 0.7573 (mmtm) cc_final: 0.7236 (ptmm) REVERT: B 1109 LEU cc_start: 0.7477 (mp) cc_final: 0.7065 (tp) REVERT: B 1220 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7101 (pt0) outliers start: 35 outliers final: 16 residues processed: 212 average time/residue: 0.2413 time to fit residues: 66.0985 Evaluate side-chains 154 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 842 LYS Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1080 LYS Chi-restraints excluded: chain B residue 1220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.0060 chunk 92 optimal weight: 0.0980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8365 Z= 0.181 Angle : 0.580 7.382 11360 Z= 0.297 Chirality : 0.039 0.144 1335 Planarity : 0.006 0.072 1390 Dihedral : 9.371 76.295 1172 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 2.38 % Allowed : 8.17 % Favored : 89.44 % 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 (0.27), residues: 1019 helix: 0.87 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.004 0.000 HIS A 850 PHE 0.009 0.001 PHE A1135 TYR 0.010 0.001 TYR B 841 ARG 0.003 0.000 ARG A1200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 0.825 Fit side-chains REVERT: A 935 ILE cc_start: 0.8170 (mt) cc_final: 0.7930 (mm) REVERT: A 947 MET cc_start: 0.8296 (mmt) cc_final: 0.7882 (mmt) REVERT: A 993 MET cc_start: 0.7480 (tpt) cc_final: 0.7228 (tpt) REVERT: A 1045 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7934 (tp) REVERT: A 1080 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6899 (mptt) REVERT: B 749 LEU cc_start: 0.8654 (tp) cc_final: 0.8444 (tp) REVERT: B 925 ARG cc_start: 0.7222 (mtm-85) cc_final: 0.6854 (mtm180) REVERT: B 935 ILE cc_start: 0.8170 (mt) cc_final: 0.7947 (mm) REVERT: B 993 MET cc_start: 0.7389 (tpt) cc_final: 0.7157 (tpt) REVERT: B 1109 LEU cc_start: 0.7547 (mp) cc_final: 0.7203 (tp) outliers start: 21 outliers final: 10 residues processed: 145 average time/residue: 0.2031 time to fit residues: 40.5187 Evaluate side-chains 137 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8365 Z= 0.253 Angle : 0.595 8.567 11360 Z= 0.299 Chirality : 0.041 0.163 1335 Planarity : 0.006 0.086 1390 Dihedral : 7.218 72.037 1127 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 2.16 % Allowed : 9.19 % Favored : 88.65 % 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 (0.26), residues: 1019 helix: 0.83 (0.22), residues: 638 sheet: None (None), residues: 0 loop : -1.17 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.003 0.001 HIS B1149 PHE 0.021 0.002 PHE A1135 TYR 0.008 0.002 TYR A 789 ARG 0.006 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.959 Fit side-chains REVERT: A 916 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 993 MET cc_start: 0.7689 (tpt) cc_final: 0.7414 (tpt) REVERT: A 1045 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7773 (tp) REVERT: A 1080 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6477 (mmmt) REVERT: B 925 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7197 (mtm180) REVERT: B 993 MET cc_start: 0.7576 (tpt) cc_final: 0.7321 (tpt) REVERT: B 1109 LEU cc_start: 0.7747 (mp) cc_final: 0.7501 (tt) outliers start: 19 outliers final: 13 residues processed: 141 average time/residue: 0.2094 time to fit residues: 39.9377 Evaluate side-chains 130 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0010 chunk 48 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 98 optimal weight: 0.0030 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN A1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8365 Z= 0.138 Angle : 0.488 7.348 11360 Z= 0.242 Chirality : 0.037 0.139 1335 Planarity : 0.005 0.066 1390 Dihedral : 6.700 68.337 1127 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 1.36 % Allowed : 10.22 % Favored : 88.42 % 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: 0.56 (0.27), residues: 1019 helix: 1.17 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.001 0.000 HIS B 853 PHE 0.008 0.001 PHE B 822 TYR 0.007 0.001 TYR A 837 ARG 0.006 0.000 ARG B1211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.925 Fit side-chains REVERT: A 742 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 916 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 993 MET cc_start: 0.7659 (tpt) cc_final: 0.7413 (tpt) REVERT: A 1011 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6376 (tt0) REVERT: B 925 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7172 (mtm180) REVERT: B 993 MET cc_start: 0.7557 (tpt) cc_final: 0.7303 (tpt) REVERT: B 1109 LEU cc_start: 0.7681 (mp) cc_final: 0.7458 (tt) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.1968 time to fit residues: 36.6233 Evaluate side-chains 133 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1153 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 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 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8365 Z= 0.171 Angle : 0.498 8.019 11360 Z= 0.246 Chirality : 0.038 0.138 1335 Planarity : 0.006 0.068 1390 Dihedral : 6.134 65.167 1121 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 2.27 % Allowed : 9.42 % Favored : 88.31 % 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: 0.68 (0.27), residues: 1019 helix: 1.22 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -0.86 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.001 0.000 HIS A1149 PHE 0.011 0.001 PHE A1135 TYR 0.008 0.001 TYR A 837 ARG 0.006 0.000 ARG B1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.912 Fit side-chains REVERT: A 742 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: A 916 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 993 MET cc_start: 0.7705 (tpt) cc_final: 0.7453 (tpt) REVERT: A 1011 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6397 (tt0) REVERT: A 1073 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7210 (ttmm) REVERT: B 925 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7242 (mtm180) REVERT: B 993 MET cc_start: 0.7595 (tpt) cc_final: 0.7202 (tpt) REVERT: B 1109 LEU cc_start: 0.7764 (mp) cc_final: 0.7544 (tt) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 0.2046 time to fit residues: 37.7757 Evaluate side-chains 128 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 845 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8365 Z= 0.200 Angle : 0.516 7.704 11360 Z= 0.256 Chirality : 0.039 0.140 1335 Planarity : 0.006 0.065 1390 Dihedral : 5.974 61.702 1121 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 2.16 % Allowed : 10.10 % Favored : 87.74 % 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: 0.68 (0.27), residues: 1019 helix: 1.22 (0.22), residues: 641 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.002 0.001 HIS A1149 PHE 0.010 0.001 PHE A1135 TYR 0.008 0.001 TYR A 837 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.889 Fit side-chains REVERT: A 742 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 916 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7567 (t80) REVERT: A 993 MET cc_start: 0.7717 (tpt) cc_final: 0.7442 (tpt) REVERT: A 1073 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6994 (ttmm) REVERT: A 1082 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7076 (ptmm) REVERT: B 925 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7277 (mtm180) REVERT: B 993 MET cc_start: 0.7643 (tpt) cc_final: 0.7252 (tpt) outliers start: 19 outliers final: 14 residues processed: 134 average time/residue: 0.2108 time to fit residues: 38.3654 Evaluate side-chains 137 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8365 Z= 0.163 Angle : 0.502 8.133 11360 Z= 0.243 Chirality : 0.038 0.135 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.815 58.967 1121 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 10.22 % Favored : 87.85 % 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: 0.86 (0.27), residues: 1019 helix: 1.33 (0.22), residues: 640 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 795 HIS 0.001 0.000 HIS B1149 PHE 0.007 0.001 PHE A 822 TYR 0.008 0.001 TYR A 837 ARG 0.007 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.874 Fit side-chains REVERT: A 916 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7558 (t80) REVERT: A 993 MET cc_start: 0.7750 (tpt) cc_final: 0.7364 (tpt) REVERT: A 1011 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6356 (tt0) REVERT: B 702 ASP cc_start: 0.7326 (t0) cc_final: 0.7114 (t0) REVERT: B 925 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7260 (mtm180) REVERT: B 993 MET cc_start: 0.7667 (tpt) cc_final: 0.7338 (tpt) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.2087 time to fit residues: 37.6566 Evaluate side-chains 141 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8365 Z= 0.213 Angle : 0.539 8.585 11360 Z= 0.262 Chirality : 0.039 0.149 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.711 57.493 1118 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 2.04 % Allowed : 10.33 % Favored : 87.63 % 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: 0.77 (0.27), residues: 1019 helix: 1.24 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -0.69 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.002 0.001 HIS B1149 PHE 0.010 0.001 PHE A1135 TYR 0.009 0.001 TYR A 837 ARG 0.008 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.968 Fit side-chains REVERT: A 916 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 993 MET cc_start: 0.7765 (tpt) cc_final: 0.7366 (tpt) REVERT: A 1082 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7079 (ptmm) REVERT: B 925 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7294 (mtm180) REVERT: B 993 MET cc_start: 0.7735 (tpt) cc_final: 0.7357 (tpt) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1991 time to fit residues: 36.0970 Evaluate side-chains 139 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 GLN B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8365 Z= 0.164 Angle : 0.520 10.482 11360 Z= 0.248 Chirality : 0.038 0.137 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.597 55.714 1118 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 10.90 % Favored : 87.17 % 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: 0.93 (0.27), residues: 1019 helix: 1.36 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.001 0.000 HIS A1149 PHE 0.007 0.001 PHE B1135 TYR 0.008 0.001 TYR A 837 ARG 0.008 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.001 Fit side-chains REVERT: A 702 ASP cc_start: 0.7250 (t0) cc_final: 0.6998 (t0) REVERT: A 916 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 993 MET cc_start: 0.7794 (tpt) cc_final: 0.7423 (tpt) REVERT: A 1011 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6357 (tt0) REVERT: A 1075 VAL cc_start: 0.4971 (OUTLIER) cc_final: 0.4500 (t) REVERT: A 1082 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7123 (ptmm) REVERT: B 925 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7269 (mtm180) REVERT: B 993 MET cc_start: 0.7694 (tpt) cc_final: 0.7385 (tpt) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.1980 time to fit residues: 37.5985 Evaluate side-chains 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 GLN B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8365 Z= 0.169 Angle : 0.520 9.670 11360 Z= 0.249 Chirality : 0.038 0.144 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.537 55.572 1118 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.70 % Allowed : 11.24 % Favored : 87.06 % 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: 0.96 (0.27), residues: 1019 helix: 1.39 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.001 0.000 HIS B1149 PHE 0.008 0.001 PHE A 822 TYR 0.008 0.001 TYR A 837 ARG 0.009 0.000 ARG B 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.927 Fit side-chains REVERT: A 702 ASP cc_start: 0.7385 (t0) cc_final: 0.7158 (t0) REVERT: A 916 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 993 MET cc_start: 0.7808 (tpt) cc_final: 0.7443 (tpt) REVERT: A 1011 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6342 (tt0) REVERT: A 1075 VAL cc_start: 0.5069 (OUTLIER) cc_final: 0.4570 (t) REVERT: A 1082 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7038 (ptmm) REVERT: B 925 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7289 (mtm180) REVERT: B 993 MET cc_start: 0.7769 (tpt) cc_final: 0.7457 (tpt) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.1980 time to fit residues: 37.1904 Evaluate side-chains 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 GLN B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097908 restraints weight = 8583.161| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.84 r_work: 0.2848 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8365 Z= 0.206 Angle : 0.541 9.690 11360 Z= 0.261 Chirality : 0.039 0.151 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.589 55.377 1118 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.82 % Allowed : 11.01 % Favored : 87.17 % 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: 0.86 (0.26), residues: 1019 helix: 1.32 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -0.69 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.002 0.000 HIS A1149 PHE 0.010 0.001 PHE A1135 TYR 0.009 0.001 TYR A 837 ARG 0.009 0.000 ARG B 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.70 seconds wall clock time: 36 minutes 35.91 seconds (2195.91 seconds total)