Starting phenix.real_space_refine on Sat Dec 9 21:55:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e14_27823/12_2023/8e14_27823.pdb" } resolution = 3.36 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= 0.001 sd= 0.054 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 154 5.49 5 S 28 5.16 5 C 7398 2.51 5 N 2309 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 253": "OD1" <-> "OD2" Residue "D VAL 265": "CG1" <-> "CG2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12442 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 869 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "J" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 318 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 869 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "M" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "N" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 318 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 283 SG CYS A 37 51.205 29.371 68.936 1.00212.62 S ATOM 306 SG CYS A 40 52.839 32.147 70.998 1.00202.14 S ATOM 4869 SG CYS E 37 91.975 74.210 70.160 1.00216.70 S ATOM 4892 SG CYS E 40 91.930 70.341 70.223 1.00213.90 S Time building chain proxies: 6.51, per 1000 atoms: 0.52 Number of scatterers: 12442 At special positions: 0 Unit cell: (146.16, 107.88, 132.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 154 15.00 O 2551 8.00 N 2309 7.00 C 7398 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=0, symmetry=0 Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 37 " Number of angles added : 3 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 30.4% alpha, 14.4% beta 72 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.540A pdb=" N GLU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 172 removed outlier: 3.892A pdb=" N ARG A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.534A pdb=" N ALA A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.811A pdb=" N TRP A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 113 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.728A pdb=" N TRP B 138 " --> pdb=" O TRP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.574A pdb=" N ARG B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 removed outlier: 3.579A pdb=" N LYS B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 185 through 198 removed outlier: 3.712A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.679A pdb=" N ASP E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 10 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.819A pdb=" N HIS E 103 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TRP E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.650A pdb=" N LEU E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 197 removed outlier: 3.700A pdb=" N ALA E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'F' and resid 98 through 113 removed outlier: 4.228A pdb=" N GLN F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 139 removed outlier: 3.677A pdb=" N TRP F 138 " --> pdb=" O TRP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 174 removed outlier: 4.297A pdb=" N ALA F 159 " --> pdb=" O MET F 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 removed outlier: 3.990A pdb=" N LYS F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 214 Processing helix chain 'F' and resid 263 through 265 No H-bonds generated for 'chain 'F' and resid 263 through 265' Processing helix chain 'G' and resid 263 through 265 No H-bonds generated for 'chain 'G' and resid 263 through 265' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 removed outlier: 3.948A pdb=" N GLY A 236 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 224 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 66 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.625A pdb=" N ILE B 118 " --> pdb=" O THR B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 258 removed outlier: 5.022A pdb=" N GLY B 236 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 224 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 258 through 261 removed outlier: 6.790A pdb=" N TYR C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP C 242 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA C 248 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 228 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY C 236 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 224 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 258 through 261 removed outlier: 4.245A pdb=" N TRP D 237 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 61 through 67 Processing sheet with id=AA9, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.175A pdb=" N ILE E 118 " --> pdb=" O THR E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 226 through 227 removed outlier: 3.671A pdb=" N ILE E 226 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 237 through 241 removed outlier: 3.628A pdb=" N LEU E 240 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA E 248 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 88 through 91 removed outlier: 6.664A pdb=" N TRP F 61 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 223 through 224 removed outlier: 3.900A pdb=" N VAL F 260 " --> pdb=" O ALA F 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 239 through 241 removed outlier: 7.030A pdb=" N ALA G 248 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 224 through 225 287 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2 1.15 - 1.32: 1693 1.32 - 1.48: 6230 1.48 - 1.65: 5099 1.65 - 1.82: 48 Bond restraints: 13072 Sorted by residual: bond pdb=" CG ASP C 253 " pdb=" OD1 ASP C 253 " ideal model delta sigma weight residual 1.249 1.529 -0.280 1.90e-02 2.77e+03 2.17e+02 bond pdb=" CG ASP E 255 " pdb=" OD2 ASP E 255 " ideal model delta sigma weight residual 1.249 1.516 -0.267 1.90e-02 2.77e+03 1.97e+02 bond pdb=" CG ASP E 255 " pdb=" OD1 ASP E 255 " ideal model delta sigma weight residual 1.249 0.983 0.266 1.90e-02 2.77e+03 1.96e+02 bond pdb=" CA VAL D 265 " pdb=" C VAL D 265 " ideal model delta sigma weight residual 1.522 1.660 -0.138 1.19e-02 7.06e+03 1.35e+02 bond pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 1.249 1.037 0.212 1.90e-02 2.77e+03 1.25e+02 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 80.17 - 100.12: 27 100.12 - 120.07: 12866 120.07 - 140.02: 5531 140.02 - 159.97: 0 159.97 - 179.92: 2 Bond angle restraints: 18426 Sorted by residual: angle pdb=" CB ASP E 255 " pdb=" CG ASP E 255 " pdb=" OD1 ASP E 255 " ideal model delta sigma weight residual 118.40 179.92 -61.52 2.30e+00 1.89e-01 7.16e+02 angle pdb=" CB ASP C 253 " pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 118.40 178.41 -60.01 2.30e+00 1.89e-01 6.81e+02 angle pdb=" CA ASP C 253 " pdb=" CB ASP C 253 " pdb=" CG ASP C 253 " ideal model delta sigma weight residual 112.60 94.33 18.27 1.00e+00 1.00e+00 3.34e+02 angle pdb=" OD1 ASP E 255 " pdb=" CG ASP E 255 " pdb=" OD2 ASP E 255 " ideal model delta sigma weight residual 122.90 80.17 42.73 2.40e+00 1.74e-01 3.17e+02 angle pdb=" OD1 ASP C 253 " pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 122.90 80.68 42.22 2.40e+00 1.74e-01 3.10e+02 ... (remaining 18421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6605 35.97 - 71.93: 765 71.93 - 107.90: 16 107.90 - 143.86: 7 143.86 - 179.83: 6 Dihedral angle restraints: 7399 sinusoidal: 4098 harmonic: 3301 Sorted by residual: dihedral pdb=" C VAL D 265 " pdb=" N VAL D 265 " pdb=" CA VAL D 265 " pdb=" CB VAL D 265 " ideal model delta harmonic sigma weight residual -122.00 -97.01 -24.99 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" CA PRO B 73 " pdb=" C PRO B 73 " pdb=" N ARG B 74 " pdb=" CA ARG B 74 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA VAL E 101 " pdb=" C VAL E 101 " pdb=" N GLN E 102 " pdb=" CA GLN E 102 " ideal model delta harmonic sigma weight residual 180.00 149.36 30.64 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 7396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.616: 2034 0.616 - 1.231: 1 1.231 - 1.847: 0 1.847 - 2.462: 0 2.462 - 3.078: 1 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CB VAL D 265 " pdb=" CA VAL D 265 " pdb=" CG1 VAL D 265 " pdb=" CG2 VAL D 265 " both_signs ideal model delta sigma weight residual False -2.63 0.45 -3.08 2.00e-01 2.50e+01 2.37e+02 chirality pdb=" CA VAL D 265 " pdb=" N VAL D 265 " pdb=" C VAL D 265 " pdb=" CB VAL D 265 " both_signs ideal model delta sigma weight residual False 2.44 3.37 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA ASP E 255 " pdb=" N ASP E 255 " pdb=" C ASP E 255 " pdb=" CB ASP E 255 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2033 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 233 " -0.045 2.00e-02 2.50e+03 4.83e-02 5.84e+01 pdb=" CG TRP H 233 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP H 233 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP H 233 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP H 233 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 233 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 233 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 233 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 233 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 233 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 222 " -0.114 5.00e-02 4.00e+02 1.52e-01 3.69e+01 pdb=" N PRO D 223 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 232 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" CD GLU D 232 " 0.077 2.00e-02 2.50e+03 pdb=" OE1 GLU D 232 " -0.028 2.00e-02 2.50e+03 pdb=" OE2 GLU D 232 " -0.026 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 995 2.73 - 3.27: 12344 3.27 - 3.81: 22571 3.81 - 4.36: 24812 4.36 - 4.90: 38546 Nonbonded interactions: 99268 Sorted by model distance: nonbonded pdb=" NE2 HIS B 93 " pdb=" O ARG B 95 " model vdw 2.182 2.520 nonbonded pdb=" OD1 ASP B 64 " pdb=" N PHE B 65 " model vdw 2.233 2.520 nonbonded pdb=" N GLU G 229 " pdb=" OE1 GLU G 229 " model vdw 2.238 2.520 nonbonded pdb=" O ARG H 227 " pdb=" NZ LYS H 264 " model vdw 2.242 2.520 nonbonded pdb=" O ARG H 244 " pdb=" OG SER H 262 " model vdw 2.257 2.440 ... (remaining 99263 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 57 through 269) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } 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: 2.390 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: 7.590 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.860 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.007 0.280 13072 Z= 0.446 Angle : 1.124 61.523 18426 Z= 0.580 Chirality : 0.083 3.078 2036 Planarity : 0.006 0.152 1774 Dihedral : 24.724 179.828 5263 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 0.41 % Allowed : 36.16 % Favored : 63.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.24), residues: 1145 helix: 0.29 (0.31), residues: 300 sheet: -1.47 (0.36), residues: 183 loop : -3.26 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.001 TRP H 233 HIS 0.006 0.001 HIS B 93 PHE 0.005 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.034 0.001 ARG H 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.3546 time to fit residues: 29.4660 Evaluate side-chains 59 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.7079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13072 Z= 0.228 Angle : 0.642 9.464 18426 Z= 0.355 Chirality : 0.041 0.208 2036 Planarity : 0.005 0.067 1774 Dihedral : 26.982 177.868 3029 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.21 % Favored : 82.79 % Rotamer: Outliers : 4.44 % Allowed : 33.57 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 1145 helix: 0.23 (0.31), residues: 303 sheet: -1.65 (0.35), residues: 189 loop : -3.27 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 PHE 0.008 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.004 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 100 average time/residue: 0.3003 time to fit residues: 41.5955 Evaluate side-chains 78 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1131 time to fit residues: 5.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 90 optimal weight: 20.0000 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13072 Z= 0.242 Angle : 0.651 9.254 18426 Z= 0.358 Chirality : 0.042 0.260 2036 Planarity : 0.005 0.058 1774 Dihedral : 26.956 177.975 3029 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.64 % Favored : 82.36 % Rotamer: Outliers : 4.34 % Allowed : 33.78 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.24), residues: 1145 helix: 0.25 (0.31), residues: 300 sheet: -1.76 (0.35), residues: 197 loop : -3.16 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 PHE 0.009 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.008 0.000 ARG H 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 61 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 97 average time/residue: 0.2862 time to fit residues: 39.0496 Evaluate side-chains 81 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1340 time to fit residues: 6.7975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13072 Z= 0.311 Angle : 0.692 9.413 18426 Z= 0.380 Chirality : 0.043 0.214 2036 Planarity : 0.005 0.056 1774 Dihedral : 27.085 175.791 3029 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.78 % Favored : 81.22 % Rotamer: Outliers : 4.75 % Allowed : 34.50 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 1145 helix: 0.05 (0.30), residues: 304 sheet: -1.90 (0.35), residues: 187 loop : -3.22 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 PHE 0.013 0.001 PHE A 199 TYR 0.018 0.001 TYR E 246 ARG 0.005 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 61 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 100 average time/residue: 0.3080 time to fit residues: 42.6380 Evaluate side-chains 82 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1478 time to fit residues: 7.1762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13072 Z= 0.206 Angle : 0.661 10.028 18426 Z= 0.361 Chirality : 0.041 0.217 2036 Planarity : 0.005 0.051 1774 Dihedral : 26.996 177.996 3029 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.55 % Favored : 82.45 % Rotamer: Outliers : 2.89 % Allowed : 34.81 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.24), residues: 1145 helix: 0.24 (0.31), residues: 300 sheet: -1.81 (0.35), residues: 189 loop : -3.09 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 233 HIS 0.004 0.001 HIS E 9 PHE 0.008 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.005 0.000 ARG H 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 85 average time/residue: 0.3253 time to fit residues: 37.5835 Evaluate side-chains 74 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1817 time to fit residues: 5.1110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13072 Z= 0.295 Angle : 0.690 9.614 18426 Z= 0.377 Chirality : 0.043 0.222 2036 Planarity : 0.005 0.050 1774 Dihedral : 27.062 175.467 3029 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer: Outliers : 2.07 % Allowed : 35.85 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1145 helix: 0.11 (0.30), residues: 302 sheet: -1.67 (0.35), residues: 180 loop : -3.15 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 PHE 0.011 0.001 PHE A 199 TYR 0.018 0.001 TYR E 246 ARG 0.005 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 81 average time/residue: 0.3238 time to fit residues: 35.7885 Evaluate side-chains 65 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1075 time to fit residues: 3.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13072 Z= 0.193 Angle : 0.664 9.609 18426 Z= 0.361 Chirality : 0.042 0.217 2036 Planarity : 0.005 0.047 1774 Dihedral : 26.960 178.223 3029 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % Rotamer: Outliers : 1.34 % Allowed : 36.67 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.24), residues: 1145 helix: 0.22 (0.30), residues: 304 sheet: -1.49 (0.36), residues: 177 loop : -3.08 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 237 HIS 0.005 0.001 HIS B 93 PHE 0.006 0.001 PHE A 199 TYR 0.015 0.001 TYR E 246 ARG 0.003 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 74 average time/residue: 0.3321 time to fit residues: 33.8512 Evaluate side-chains 65 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2004 time to fit residues: 3.3550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13072 Z= 0.208 Angle : 0.668 9.670 18426 Z= 0.363 Chirality : 0.041 0.212 2036 Planarity : 0.005 0.051 1774 Dihedral : 26.931 176.802 3029 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.47 % Favored : 82.53 % Rotamer: Outliers : 1.14 % Allowed : 36.67 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.24), residues: 1145 helix: 0.23 (0.30), residues: 306 sheet: -1.40 (0.36), residues: 183 loop : -3.13 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP H 233 HIS 0.005 0.001 HIS B 93 PHE 0.007 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.004 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 69 average time/residue: 0.3569 time to fit residues: 33.1378 Evaluate side-chains 63 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2327 time to fit residues: 2.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13072 Z= 0.193 Angle : 0.667 11.683 18426 Z= 0.360 Chirality : 0.041 0.212 2036 Planarity : 0.005 0.051 1774 Dihedral : 26.879 177.548 3029 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.21 % Favored : 82.79 % Rotamer: Outliers : 0.41 % Allowed : 37.09 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1145 helix: 0.26 (0.31), residues: 304 sheet: -1.26 (0.37), residues: 172 loop : -3.06 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 233 HIS 0.005 0.001 HIS B 93 PHE 0.005 0.001 PHE A 199 TYR 0.015 0.001 TYR E 246 ARG 0.004 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.3471 time to fit residues: 33.2265 Evaluate side-chains 64 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1167 time to fit residues: 2.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13072 Z= 0.222 Angle : 0.677 10.866 18426 Z= 0.365 Chirality : 0.041 0.208 2036 Planarity : 0.005 0.048 1774 Dihedral : 26.893 177.041 3029 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 0.21 % Allowed : 37.29 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1145 helix: 0.27 (0.31), residues: 304 sheet: -1.16 (0.36), residues: 171 loop : -3.11 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP H 233 HIS 0.005 0.001 HIS B 93 PHE 0.012 0.001 PHE E 65 TYR 0.016 0.001 TYR E 246 ARG 0.003 0.000 ARG C 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.3603 time to fit residues: 29.7298 Evaluate side-chains 61 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1168 time to fit residues: 1.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 41 optimal weight: 0.0050 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 chunk 86 optimal weight: 0.0570 overall best weight: 0.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.054620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.038541 restraints weight = 101322.667| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 5.28 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13072 Z= 0.183 Angle : 0.668 11.504 18426 Z= 0.358 Chirality : 0.041 0.211 2036 Planarity : 0.005 0.047 1774 Dihedral : 26.774 179.426 3029 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 0.21 % Allowed : 37.29 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.24), residues: 1145 helix: 0.38 (0.32), residues: 298 sheet: -0.91 (0.38), residues: 162 loop : -2.98 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 233 HIS 0.006 0.001 HIS B 93 PHE 0.006 0.001 PHE F 126 TYR 0.013 0.001 TYR E 246 ARG 0.003 0.000 ARG C 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.49 seconds wall clock time: 42 minutes 16.15 seconds (2536.15 seconds total)