Starting phenix.real_space_refine on Fri Dec 8 10:44:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/12_2023/8gv8_34287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/12_2023/8gv8_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_34287/12_2023/8gv8_34287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/12_2023/8gv8_34287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/12_2023/8gv8_34287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv8_34287/12_2023/8gv8_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-1.21rc1-5172/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: 4.83, per 1000 atoms: 0.59 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: 3.10 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: 1.48 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: 1.88 Time building geometry restraints manager: 3.39 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- 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 : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 212 average time/residue: 0.2389 time to fit residues: 65.5492 Evaluate side-chains 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1277 time to fit residues: 4.3308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 59 optimal weight: 0.0060 chunk 92 optimal weight: 0.7980 overall best weight: 0.4354 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8365 Z= 0.178 Angle : 0.590 8.348 11360 Z= 0.301 Chirality : 0.039 0.162 1335 Planarity : 0.006 0.076 1390 Dihedral : 6.652 76.893 1115 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.02 % Allowed : 8.06 % Favored : 90.92 % 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: 0.85 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -1.41 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 795 HIS 0.003 0.000 HIS A 850 PHE 0.009 0.001 PHE B 847 TYR 0.016 0.001 TYR B 841 ARG 0.003 0.000 ARG B 976 *********************** 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 144 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.969 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 139 average time/residue: 0.1982 time to fit residues: 38.4692 Evaluate side-chains 129 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0945 time to fit residues: 2.4850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8365 Z= 0.247 Angle : 0.589 8.439 11360 Z= 0.296 Chirality : 0.040 0.142 1335 Planarity : 0.006 0.083 1390 Dihedral : 6.410 72.535 1115 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 1.25 % Allowed : 9.19 % Favored : 89.56 % 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: 0.13 (0.26), residues: 1019 helix: 0.83 (0.22), residues: 640 sheet: None (None), residues: 0 loop : -1.15 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.003 0.001 HIS B1149 PHE 0.022 0.002 PHE A1135 TYR 0.008 0.001 TYR A 789 ARG 0.005 0.000 ARG B1211 *********************** 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 141 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.043 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.1858 time to fit residues: 35.7510 Evaluate side-chains 121 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0825 time to fit residues: 2.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8365 Z= 0.163 Angle : 0.513 8.181 11360 Z= 0.255 Chirality : 0.038 0.132 1335 Planarity : 0.006 0.072 1390 Dihedral : 6.157 69.398 1115 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 0.79 % Allowed : 10.22 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1019 helix: 1.01 (0.22), residues: 641 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.001 0.000 HIS B1149 PHE 0.010 0.001 PHE B1135 TYR 0.009 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 128 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.847 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 126 average time/residue: 0.1949 time to fit residues: 34.2734 Evaluate side-chains 126 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0864 time to fit residues: 2.0575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 68 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2708 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= 0.164 Angle : 0.498 8.149 11360 Z= 0.246 Chirality : 0.038 0.131 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.905 65.207 1115 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 0.79 % Allowed : 10.22 % Favored : 88.99 % 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: 0.59 (0.27), residues: 1019 helix: 1.13 (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 A 795 HIS 0.002 0.000 HIS B1149 PHE 0.010 0.001 PHE A1135 TYR 0.009 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 137 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.914 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 135 average time/residue: 0.1899 time to fit residues: 36.0686 Evaluate side-chains 119 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0761 time to fit residues: 1.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8365 Z= 0.179 Angle : 0.509 8.146 11360 Z= 0.250 Chirality : 0.038 0.141 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.791 61.435 1115 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.75 % Favored : 97.15 % Rotamer: Outliers : 0.68 % Allowed : 10.90 % 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: 0.69 (0.27), residues: 1019 helix: 1.20 (0.22), residues: 641 sheet: None (None), residues: 0 loop : -0.79 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 795 HIS 0.002 0.000 HIS B1149 PHE 0.009 0.001 PHE B 822 TYR 0.009 0.001 TYR A 837 ARG 0.007 0.000 ARG B1211 *********************** 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 127 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.982 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.1864 time to fit residues: 32.9928 Evaluate side-chains 121 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0856 time to fit residues: 2.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3026 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= 0.182 Angle : 0.514 7.986 11360 Z= 0.249 Chirality : 0.038 0.137 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.671 58.659 1115 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 0.57 % Allowed : 11.12 % 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: 0.76 (0.27), residues: 1019 helix: 1.24 (0.22), residues: 641 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.001 0.000 HIS B1149 PHE 0.009 0.001 PHE B1135 TYR 0.010 0.001 TYR A 837 ARG 0.007 0.000 ARG B 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 136 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.954 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 134 average time/residue: 0.1882 time to fit residues: 35.6564 Evaluate side-chains 126 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0833 time to fit residues: 1.8311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3104 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= 0.152 Angle : 0.503 7.405 11360 Z= 0.242 Chirality : 0.037 0.130 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.538 56.673 1115 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 0.45 % Allowed : 11.80 % 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: 0.96 (0.27), residues: 1019 helix: 1.41 (0.22), residues: 635 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.001 0.000 HIS A 695 PHE 0.007 0.001 PHE A1135 TYR 0.008 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 129 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.962 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 127 average time/residue: 0.2040 time to fit residues: 36.3483 Evaluate side-chains 124 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0783 time to fit residues: 1.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 82 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8365 Z= 0.184 Angle : 0.517 7.620 11360 Z= 0.252 Chirality : 0.038 0.143 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.531 55.543 1115 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 0.45 % Allowed : 11.69 % 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: 0.88 (0.27), residues: 1019 helix: 1.31 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -0.62 (0.30), 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 0.009 0.001 PHE B1135 TYR 0.010 0.001 TYR A 837 ARG 0.008 0.000 ARG A 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 128 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.908 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.1980 time to fit residues: 35.4342 Evaluate side-chains 120 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0823 time to fit residues: 1.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3222 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= 0.150 Angle : 0.494 7.284 11360 Z= 0.240 Chirality : 0.037 0.135 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.404 56.030 1115 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 0.11 % Allowed : 12.15 % 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: 1.10 (0.27), residues: 1019 helix: 1.50 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -0.54 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.001 0.000 HIS B1149 PHE 0.007 0.001 PHE A1135 TYR 0.008 0.001 TYR A 837 ARG 0.010 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 133 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.015 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2272 time to fit residues: 42.9263 Evaluate side-chains 125 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 GLN B 735 GLN B1089 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100597 restraints weight = 8578.013| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.85 r_work: 0.2870 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8365 Z= 0.156 Angle : 0.498 7.480 11360 Z= 0.241 Chirality : 0.038 0.135 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.349 56.854 1115 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.23 % Allowed : 12.60 % 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: 1.13 (0.27), residues: 1019 helix: 1.49 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -0.48 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.008 0.000 ARG A 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.99 seconds wall clock time: 37 minutes 26.80 seconds (2246.80 seconds total)