Starting phenix.real_space_refine on Sun Apr 7 06:49:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bri_16215/04_2024/8bri_16215.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 92 5.16 5 C 6392 2.51 5 N 1625 2.21 5 O 1802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 43": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9911 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1880 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "B" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1761 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "C" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1888 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain: "D" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1825 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1761 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "F" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 398 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "G" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 398 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9911 At special positions: 0 Unit cell: (99.008, 109.824, 113.152, 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 92 16.00 O 1802 8.00 N 1625 7.00 C 6392 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: 4.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 1 sheets defined 87.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 74 through 91 Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.918A pdb=" N ASP A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 167 removed outlier: 3.578A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 174 through 196 removed outlier: 4.006A pdb=" N THR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 228 Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.761A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.551A pdb=" N ILE A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 50 Processing helix chain 'B' and resid 51 through 68 Processing helix chain 'B' and resid 72 through 90 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.945A pdb=" N GLU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 117 through 168 Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 171 through 196 removed outlier: 3.586A pdb=" N GLY B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.554A pdb=" N THR B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 227 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 241 through 244 removed outlier: 3.805A pdb=" N GLU B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.946A pdb=" N LEU B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.743A pdb=" N LYS C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 68 Processing helix chain 'C' and resid 72 through 91 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.875A pdb=" N GLU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 117 through 168 Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 175 through 196 removed outlier: 4.013A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'D' and resid 2 through 23 removed outlier: 3.654A pdb=" N GLY D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.582A pdb=" N VAL D 30 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.519A pdb=" N LEU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.545A pdb=" N GLU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 117 through 168 Proline residue: D 151 - end of helix removed outlier: 3.865A pdb=" N ASN D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.557A pdb=" N ALA D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.600A pdb=" N MET E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 48 Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 91 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 Proline residue: E 177 - end of helix removed outlier: 3.704A pdb=" N THR E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 227 Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.671A pdb=" N SER E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.591A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU E 249 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.886A pdb=" N GLY F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 removed outlier: 3.666A pdb=" N LYS F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 39 removed outlier: 4.523A pdb=" N THR G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 Processing sheet with id=AA1, first strand: chain 'F' and resid 40 through 42 868 hydrogen bonds defined for protein. 2574 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: 3.01 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1778 1.32 - 1.45: 2242 1.45 - 1.57: 5854 1.57 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 10056 Sorted by residual: bond pdb=" CG GLN D 210 " pdb=" CD GLN D 210 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.14e+00 bond pdb=" CB ILE D 156 " pdb=" CG2 ILE D 156 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CB VAL G 34 " pdb=" CG1 VAL G 34 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CG MET F 30 " pdb=" SD MET F 30 " ideal model delta sigma weight residual 1.803 1.756 0.047 2.50e-02 1.60e+03 3.54e+00 bond pdb=" CG MET A 169 " pdb=" SD MET A 169 " ideal model delta sigma weight residual 1.803 1.756 0.047 2.50e-02 1.60e+03 3.49e+00 ... (remaining 10051 not shown) Histogram of bond angle deviations from ideal: 92.98 - 101.20: 73 101.20 - 109.42: 696 109.42 - 117.65: 6508 117.65 - 125.87: 6180 125.87 - 134.10: 84 Bond angle restraints: 13541 Sorted by residual: angle pdb=" O PHE F 58 " pdb=" C PHE F 58 " pdb=" N GLY F 59 " ideal model delta sigma weight residual 122.19 100.62 21.57 1.21e+00 6.83e-01 3.18e+02 angle pdb=" CA MET B 219 " pdb=" CB MET B 219 " pdb=" CG MET B 219 " ideal model delta sigma weight residual 114.10 128.24 -14.14 2.00e+00 2.50e-01 5.00e+01 angle pdb=" CA MET D 83 " pdb=" CB MET D 83 " pdb=" CG MET D 83 " ideal model delta sigma weight residual 114.10 128.10 -14.00 2.00e+00 2.50e-01 4.90e+01 angle pdb=" CA MET C 219 " pdb=" CB MET C 219 " pdb=" CG MET C 219 " ideal model delta sigma weight residual 114.10 127.70 -13.60 2.00e+00 2.50e-01 4.62e+01 angle pdb=" CA MET C 83 " pdb=" CB MET C 83 " pdb=" CG MET C 83 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.90e+01 ... (remaining 13536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5201 17.64 - 35.28: 670 35.28 - 52.92: 152 52.92 - 70.56: 18 70.56 - 88.20: 15 Dihedral angle restraints: 6056 sinusoidal: 2374 harmonic: 3682 Sorted by residual: dihedral pdb=" CA GLU D 99 " pdb=" C GLU D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" N GLN D 210 " pdb=" C GLN D 210 " pdb=" CA GLN D 210 " pdb=" CB GLN D 210 " ideal model delta harmonic sigma weight residual 122.80 133.25 -10.45 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" N MET E 83 " pdb=" C MET E 83 " pdb=" CA MET E 83 " pdb=" CB MET E 83 " ideal model delta harmonic sigma weight residual 122.80 133.11 -10.31 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1506 0.122 - 0.243: 73 0.243 - 0.365: 15 0.365 - 0.487: 1 0.487 - 0.608: 1 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CG LEU D 213 " pdb=" CB LEU D 213 " pdb=" CD1 LEU D 213 " pdb=" CD2 LEU D 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1593 not shown) Planarity restraints: 1725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 58 " 0.089 2.00e-02 2.50e+03 1.54e-01 2.39e+02 pdb=" C PHE F 58 " -0.268 2.00e-02 2.50e+03 pdb=" O PHE F 58 " 0.095 2.00e-02 2.50e+03 pdb=" N GLY F 59 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 58 " 0.037 2.00e-02 2.50e+03 7.20e-02 5.19e+01 pdb=" C PHE G 58 " -0.125 2.00e-02 2.50e+03 pdb=" O PHE G 58 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY G 59 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 44 " -0.024 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE D 44 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 44 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 44 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 44 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE D 44 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 1722 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 84 2.55 - 3.14: 8640 3.14 - 3.73: 17280 3.73 - 4.31: 21721 4.31 - 4.90: 35416 Nonbonded interactions: 83141 Sorted by model distance: nonbonded pdb=" OG SER D 193 " pdb=" OD1 ASN D 194 " model vdw 1.969 2.440 nonbonded pdb=" O PHE C 29 " pdb=" OH TYR C 188 " model vdw 2.167 2.440 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASN E 101 " pdb=" N ASN E 102 " model vdw 2.189 2.520 nonbonded pdb=" NZ LYS C 107 " pdb=" OD2 ASP C 128 " model vdw 2.207 2.520 ... (remaining 83136 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 20 through 243) selection = (chain 'B' and resid 20 through 243) selection = (chain 'C' and resid 20 through 243) selection = (chain 'D' and resid 20 through 243) selection = (chain 'E' and resid 20 through 243) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.650 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: 13.440 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.005 0.069 10056 Z= 0.348 Angle : 1.304 21.571 13541 Z= 0.665 Chirality : 0.066 0.608 1596 Planarity : 0.007 0.154 1725 Dihedral : 16.369 88.201 3694 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.15 % Allowed : 30.13 % Favored : 68.71 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1298 helix: 1.84 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP G 18 HIS 0.003 0.001 HIS C 116 PHE 0.065 0.002 PHE D 44 TYR 0.042 0.003 TYR B 237 ARG 0.010 0.001 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 286 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6890 (tm-30) REVERT: B 138 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: C 169 MET cc_start: 0.7424 (tmm) cc_final: 0.7222 (tmm) REVERT: C 208 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7957 (ttp-110) REVERT: D 134 GLU cc_start: 0.8411 (pp20) cc_final: 0.7583 (pp20) REVERT: E 39 VAL cc_start: 0.7848 (t) cc_final: 0.7645 (p) REVERT: E 169 MET cc_start: 0.8246 (ppp) cc_final: 0.7884 (ttp) outliers start: 12 outliers final: 4 residues processed: 290 average time/residue: 0.2471 time to fit residues: 99.3129 Evaluate side-chains 269 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 264 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 99 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10056 Z= 0.228 Angle : 0.792 9.978 13541 Z= 0.392 Chirality : 0.044 0.251 1596 Planarity : 0.004 0.040 1725 Dihedral : 5.157 55.903 1383 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.32 % Allowed : 22.17 % Favored : 73.51 % 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: 1.66 (0.23), residues: 1298 helix: 1.51 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 PHE 0.028 0.002 PHE F 32 TYR 0.033 0.002 TYR B 237 ARG 0.007 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8734 (mpp) cc_final: 0.8489 (mpp) REVERT: B 134 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 138 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8700 (mm-40) REVERT: B 169 MET cc_start: 0.6983 (tmm) cc_final: 0.6609 (tmm) REVERT: C 56 PHE cc_start: 0.7164 (m-80) cc_final: 0.6856 (m-80) REVERT: C 208 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7875 (ttp-110) REVERT: D 15 PHE cc_start: 0.8289 (m-80) cc_final: 0.8069 (m-80) REVERT: D 83 MET cc_start: 0.9308 (mmm) cc_final: 0.9062 (mmm) REVERT: D 159 LEU cc_start: 0.9085 (mm) cc_final: 0.8859 (mm) REVERT: D 208 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8365 (ttp80) REVERT: D 211 GLU cc_start: 0.8981 (tp30) cc_final: 0.8755 (tp30) REVERT: D 229 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6661 (pp30) REVERT: E 68 PHE cc_start: 0.7646 (m-80) cc_final: 0.7348 (m-10) REVERT: E 117 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7552 (p0) REVERT: E 153 MET cc_start: 0.8779 (mmm) cc_final: 0.8431 (tpp) REVERT: E 165 MET cc_start: 0.8359 (mtm) cc_final: 0.8157 (ttm) REVERT: E 211 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 19 MET cc_start: 0.8369 (tpt) cc_final: 0.8149 (tpt) REVERT: F 26 MET cc_start: 0.9418 (mmm) cc_final: 0.9129 (mmt) REVERT: G 55 LYS cc_start: 0.7021 (mmtp) cc_final: 0.6798 (mmtt) outliers start: 45 outliers final: 22 residues processed: 313 average time/residue: 0.2287 time to fit residues: 99.5643 Evaluate side-chains 283 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 259 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 0.0670 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN G 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10056 Z= 0.214 Angle : 0.753 11.762 13541 Z= 0.372 Chirality : 0.042 0.220 1596 Planarity : 0.004 0.037 1725 Dihedral : 4.407 53.623 1372 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.65 % Allowed : 25.05 % Favored : 71.31 % 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: 1.60 (0.23), residues: 1298 helix: 1.47 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -1.28 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 PHE 0.026 0.002 PHE F 32 TYR 0.021 0.001 TYR B 237 ARG 0.005 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.4164 (mtp) cc_final: 0.3881 (mtt) REVERT: B 134 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7263 (tm-30) REVERT: B 153 MET cc_start: 0.8536 (tpp) cc_final: 0.7936 (tpp) REVERT: B 155 MET cc_start: 0.9101 (tpp) cc_final: 0.8593 (tpp) REVERT: C 56 PHE cc_start: 0.7204 (m-80) cc_final: 0.6913 (m-10) REVERT: C 74 GLU cc_start: 0.8762 (pm20) cc_final: 0.8536 (pm20) REVERT: D 83 MET cc_start: 0.9326 (mmm) cc_final: 0.9079 (mmm) REVERT: D 99 GLU cc_start: 0.8420 (mp0) cc_final: 0.8163 (pm20) REVERT: D 211 GLU cc_start: 0.8976 (tp30) cc_final: 0.8771 (tp30) REVERT: E 68 PHE cc_start: 0.7692 (m-80) cc_final: 0.7102 (m-10) REVERT: E 105 MET cc_start: 0.8988 (tpt) cc_final: 0.8714 (tpp) REVERT: E 117 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7499 (p0) REVERT: E 153 MET cc_start: 0.8733 (mmm) cc_final: 0.8453 (tpp) REVERT: E 214 ASN cc_start: 0.8932 (m110) cc_final: 0.8669 (p0) outliers start: 38 outliers final: 20 residues processed: 307 average time/residue: 0.2158 time to fit residues: 92.8923 Evaluate side-chains 280 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 0.0270 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10056 Z= 0.189 Angle : 0.746 12.292 13541 Z= 0.363 Chirality : 0.042 0.272 1596 Planarity : 0.004 0.038 1725 Dihedral : 4.160 18.559 1369 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.74 % Allowed : 26.10 % Favored : 70.15 % 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: 1.63 (0.23), residues: 1298 helix: 1.50 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 18 HIS 0.002 0.001 HIS D 136 PHE 0.022 0.001 PHE F 39 TYR 0.017 0.001 TYR B 237 ARG 0.006 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 291 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8694 (mpp) cc_final: 0.8379 (mpp) REVERT: A 98 MET cc_start: 0.4206 (mtp) cc_final: 0.3823 (mtt) REVERT: A 134 GLU cc_start: 0.8124 (pp20) cc_final: 0.7863 (pp20) REVERT: B 122 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8740 (ttp80) REVERT: B 134 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 153 MET cc_start: 0.8520 (tpp) cc_final: 0.8126 (tpp) REVERT: C 52 MET cc_start: 0.8333 (tpp) cc_final: 0.8118 (tpp) REVERT: C 56 PHE cc_start: 0.7200 (m-80) cc_final: 0.6930 (m-10) REVERT: C 61 ILE cc_start: 0.8557 (tp) cc_final: 0.8250 (tp) REVERT: C 104 PHE cc_start: 0.8333 (t80) cc_final: 0.7687 (t80) REVERT: C 247 ARG cc_start: 0.8335 (mmm160) cc_final: 0.8107 (mmm-85) REVERT: D 83 MET cc_start: 0.9310 (mmm) cc_final: 0.8958 (mmm) REVERT: D 99 GLU cc_start: 0.8500 (mp0) cc_final: 0.8150 (pm20) REVERT: D 105 MET cc_start: 0.8249 (ppp) cc_final: 0.7526 (ppp) REVERT: D 106 GLN cc_start: 0.9014 (mm110) cc_final: 0.8530 (mm-40) REVERT: D 211 GLU cc_start: 0.9001 (tp30) cc_final: 0.8609 (tp30) REVERT: D 216 ARG cc_start: 0.9300 (ttt180) cc_final: 0.9097 (tpp80) REVERT: D 219 MET cc_start: 0.8779 (ppp) cc_final: 0.8509 (ppp) REVERT: D 226 GLN cc_start: 0.8762 (mm110) cc_final: 0.8459 (mm110) REVERT: E 68 PHE cc_start: 0.7665 (m-80) cc_final: 0.7176 (m-10) REVERT: E 83 MET cc_start: 0.9053 (mpp) cc_final: 0.8851 (mpp) REVERT: E 105 MET cc_start: 0.9249 (tpt) cc_final: 0.8153 (tpt) REVERT: E 117 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7556 (p0) REVERT: E 153 MET cc_start: 0.8737 (mmm) cc_final: 0.8481 (tpt) REVERT: E 214 ASN cc_start: 0.8922 (m110) cc_final: 0.8554 (p0) REVERT: E 218 ILE cc_start: 0.8531 (mt) cc_final: 0.8099 (mm) outliers start: 39 outliers final: 20 residues processed: 314 average time/residue: 0.2198 time to fit residues: 95.2831 Evaluate side-chains 280 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN D 101 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10056 Z= 0.221 Angle : 0.756 12.904 13541 Z= 0.372 Chirality : 0.042 0.209 1596 Planarity : 0.004 0.034 1725 Dihedral : 4.155 17.814 1369 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.37 % Allowed : 25.34 % Favored : 69.29 % 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: 1.57 (0.23), residues: 1298 helix: 1.45 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -1.23 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 PHE 0.038 0.001 PHE C 104 TYR 0.021 0.002 TYR B 237 ARG 0.015 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5545 (ptt) cc_final: 0.5198 (ptp) REVERT: A 98 MET cc_start: 0.4257 (mtp) cc_final: 0.4054 (mtt) REVERT: B 122 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8737 (ttp80) REVERT: B 134 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 153 MET cc_start: 0.8550 (tpp) cc_final: 0.8169 (tpp) REVERT: B 159 LEU cc_start: 0.8981 (mp) cc_final: 0.8724 (mp) REVERT: B 194 ASN cc_start: 0.7769 (m-40) cc_final: 0.7430 (m-40) REVERT: B 210 GLN cc_start: 0.8894 (tt0) cc_final: 0.8304 (pp30) REVERT: B 211 GLU cc_start: 0.8740 (tp30) cc_final: 0.8420 (tp30) REVERT: C 50 PHE cc_start: 0.8198 (m-80) cc_final: 0.7775 (m-80) REVERT: C 52 MET cc_start: 0.8413 (tpp) cc_final: 0.8173 (tpp) REVERT: C 56 PHE cc_start: 0.7270 (m-80) cc_final: 0.6979 (m-80) REVERT: C 104 PHE cc_start: 0.8019 (t80) cc_final: 0.7677 (t80) REVERT: C 208 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.7833 (ttp-110) REVERT: D 83 MET cc_start: 0.9263 (mmm) cc_final: 0.9048 (mmm) REVERT: D 99 GLU cc_start: 0.8542 (mp0) cc_final: 0.8175 (pm20) REVERT: D 105 MET cc_start: 0.8231 (ppp) cc_final: 0.7541 (ppp) REVERT: D 106 GLN cc_start: 0.9014 (mm110) cc_final: 0.8578 (mm-40) REVERT: D 208 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8067 (ttp80) REVERT: D 211 GLU cc_start: 0.9002 (tp30) cc_final: 0.8799 (tp30) REVERT: D 216 ARG cc_start: 0.9317 (ttt180) cc_final: 0.8965 (tpp80) REVERT: D 226 GLN cc_start: 0.8772 (mm110) cc_final: 0.8503 (mm110) REVERT: E 68 PHE cc_start: 0.7610 (m-80) cc_final: 0.7116 (m-10) REVERT: E 105 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8662 (tpp) REVERT: E 117 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7556 (p0) REVERT: E 153 MET cc_start: 0.8747 (mmm) cc_final: 0.8519 (tpp) REVERT: E 165 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: E 210 GLN cc_start: 0.9153 (mt0) cc_final: 0.8868 (mp10) REVERT: E 214 ASN cc_start: 0.8942 (m110) cc_final: 0.8531 (p0) REVERT: E 218 ILE cc_start: 0.8586 (mt) cc_final: 0.8196 (mm) REVERT: G 42 MET cc_start: 0.8490 (tmm) cc_final: 0.7550 (tmm) outliers start: 56 outliers final: 34 residues processed: 306 average time/residue: 0.2167 time to fit residues: 92.9158 Evaluate side-chains 297 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10056 Z= 0.221 Angle : 0.808 14.943 13541 Z= 0.394 Chirality : 0.043 0.254 1596 Planarity : 0.004 0.034 1725 Dihedral : 4.193 17.217 1369 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.51 % Allowed : 26.68 % Favored : 68.81 % 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: 1.45 (0.23), residues: 1298 helix: 1.37 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP G 18 HIS 0.002 0.001 HIS D 136 PHE 0.045 0.001 PHE C 104 TYR 0.028 0.002 TYR A 237 ARG 0.006 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 272 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5552 (ptt) cc_final: 0.5217 (ptp) REVERT: A 83 MET cc_start: 0.8685 (mpp) cc_final: 0.8416 (mpp) REVERT: A 98 MET cc_start: 0.4360 (mtp) cc_final: 0.4005 (mtt) REVERT: B 122 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8688 (ttp80) REVERT: B 134 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7050 (tm-30) REVERT: B 153 MET cc_start: 0.8566 (tpp) cc_final: 0.8154 (tpp) REVERT: B 194 ASN cc_start: 0.7788 (m-40) cc_final: 0.7460 (m-40) REVERT: C 50 PHE cc_start: 0.8195 (m-80) cc_final: 0.7788 (m-80) REVERT: C 52 MET cc_start: 0.8431 (tpp) cc_final: 0.8157 (tpp) REVERT: C 56 PHE cc_start: 0.7280 (m-80) cc_final: 0.6965 (m-80) REVERT: C 169 MET cc_start: 0.7518 (tmm) cc_final: 0.7301 (tmm) REVERT: D 99 GLU cc_start: 0.8448 (mp0) cc_final: 0.8103 (pm20) REVERT: D 105 MET cc_start: 0.8329 (ppp) cc_final: 0.7744 (ppp) REVERT: D 106 GLN cc_start: 0.9060 (mm110) cc_final: 0.8649 (mm-40) REVERT: D 210 GLN cc_start: 0.8594 (pm20) cc_final: 0.8260 (pm20) REVERT: D 211 GLU cc_start: 0.9004 (tp30) cc_final: 0.8796 (tp30) REVERT: D 216 ARG cc_start: 0.9300 (ttt180) cc_final: 0.9069 (tpp80) REVERT: D 226 GLN cc_start: 0.8747 (mm110) cc_final: 0.8514 (mm110) REVERT: E 68 PHE cc_start: 0.7646 (m-80) cc_final: 0.7076 (m-10) REVERT: E 105 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8579 (tpp) REVERT: E 117 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7453 (p0) REVERT: E 153 MET cc_start: 0.8712 (mmm) cc_final: 0.8316 (tpt) REVERT: E 165 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7488 (mmm) REVERT: E 210 GLN cc_start: 0.9166 (mt0) cc_final: 0.8831 (mp10) REVERT: E 214 ASN cc_start: 0.8952 (m110) cc_final: 0.8616 (p0) REVERT: E 218 ILE cc_start: 0.8648 (mt) cc_final: 0.8192 (mm) outliers start: 47 outliers final: 36 residues processed: 297 average time/residue: 0.2129 time to fit residues: 88.5221 Evaluate side-chains 297 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 77 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: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10056 Z= 0.229 Angle : 0.811 13.674 13541 Z= 0.397 Chirality : 0.043 0.264 1596 Planarity : 0.004 0.035 1725 Dihedral : 4.191 19.089 1369 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.28 % Allowed : 27.16 % Favored : 67.56 % 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: 1.47 (0.23), residues: 1298 helix: 1.35 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -1.11 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 18 HIS 0.002 0.001 HIS D 136 PHE 0.034 0.002 PHE F 32 TYR 0.023 0.002 TYR A 237 ARG 0.008 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5574 (ptt) cc_final: 0.5239 (ptp) REVERT: A 74 GLU cc_start: 0.9234 (tt0) cc_final: 0.8924 (pm20) REVERT: A 179 MET cc_start: 0.8165 (tpp) cc_final: 0.7842 (tpp) REVERT: B 122 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8662 (ttp80) REVERT: B 134 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 153 MET cc_start: 0.8532 (tpp) cc_final: 0.7903 (tpp) REVERT: B 194 ASN cc_start: 0.7820 (m-40) cc_final: 0.7501 (m-40) REVERT: C 50 PHE cc_start: 0.8183 (m-80) cc_final: 0.7793 (m-80) REVERT: C 52 MET cc_start: 0.8486 (tpp) cc_final: 0.8248 (tpp) REVERT: C 56 PHE cc_start: 0.7307 (m-80) cc_final: 0.6936 (m-80) REVERT: C 169 MET cc_start: 0.7587 (tmm) cc_final: 0.7369 (tmm) REVERT: C 195 MET cc_start: 0.6051 (mtt) cc_final: 0.5820 (mtt) REVERT: D 99 GLU cc_start: 0.8480 (mp0) cc_final: 0.8108 (pm20) REVERT: D 105 MET cc_start: 0.8264 (ppp) cc_final: 0.7697 (ppp) REVERT: D 106 GLN cc_start: 0.9038 (mm110) cc_final: 0.8581 (mm-40) REVERT: D 211 GLU cc_start: 0.8993 (tp30) cc_final: 0.8570 (tp30) REVERT: D 216 ARG cc_start: 0.9299 (ttt180) cc_final: 0.9073 (tpp80) REVERT: D 219 MET cc_start: 0.8741 (ppp) cc_final: 0.8506 (ppp) REVERT: E 68 PHE cc_start: 0.7657 (m-80) cc_final: 0.7116 (m-10) REVERT: E 105 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8497 (tpp) REVERT: E 117 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7474 (p0) REVERT: E 214 ASN cc_start: 0.8978 (m110) cc_final: 0.8702 (p0) REVERT: E 218 ILE cc_start: 0.8640 (mt) cc_final: 0.8163 (mm) REVERT: F 30 MET cc_start: 0.8759 (tpp) cc_final: 0.8126 (tpt) outliers start: 55 outliers final: 39 residues processed: 291 average time/residue: 0.2282 time to fit residues: 93.8717 Evaluate side-chains 296 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 255 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10056 Z= 0.234 Angle : 0.845 13.742 13541 Z= 0.410 Chirality : 0.043 0.211 1596 Planarity : 0.004 0.036 1725 Dihedral : 4.229 19.419 1369 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.70 % Allowed : 27.74 % Favored : 67.56 % 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: 1.37 (0.23), residues: 1298 helix: 1.32 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 18 HIS 0.003 0.001 HIS D 136 PHE 0.027 0.002 PHE C 104 TYR 0.019 0.002 TYR A 237 ARG 0.010 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 259 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5561 (ptt) cc_final: 0.5271 (ptp) REVERT: A 74 GLU cc_start: 0.9209 (tt0) cc_final: 0.8899 (pm20) REVERT: A 230 ASN cc_start: 0.8892 (t0) cc_final: 0.8318 (p0) REVERT: B 122 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8656 (ttp80) REVERT: B 134 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 153 MET cc_start: 0.8521 (tpp) cc_final: 0.7846 (tpp) REVERT: B 194 ASN cc_start: 0.7786 (m-40) cc_final: 0.7489 (m-40) REVERT: B 210 GLN cc_start: 0.8858 (tt0) cc_final: 0.8298 (pp30) REVERT: B 211 GLU cc_start: 0.8823 (tp30) cc_final: 0.8471 (tp30) REVERT: C 50 PHE cc_start: 0.8181 (m-80) cc_final: 0.7754 (m-80) REVERT: C 52 MET cc_start: 0.8479 (tpp) cc_final: 0.8262 (tpp) REVERT: C 56 PHE cc_start: 0.7301 (m-80) cc_final: 0.6892 (m-80) REVERT: C 169 MET cc_start: 0.7540 (tmm) cc_final: 0.7339 (tmm) REVERT: C 195 MET cc_start: 0.6063 (mtt) cc_final: 0.5847 (mtt) REVERT: D 99 GLU cc_start: 0.8525 (mp0) cc_final: 0.8186 (pm20) REVERT: D 105 MET cc_start: 0.8267 (ppp) cc_final: 0.7677 (ppp) REVERT: D 106 GLN cc_start: 0.9027 (mm110) cc_final: 0.8590 (mm-40) REVERT: D 169 MET cc_start: 0.7622 (mmm) cc_final: 0.7407 (mmt) REVERT: D 211 GLU cc_start: 0.8986 (tp30) cc_final: 0.8753 (tp30) REVERT: D 216 ARG cc_start: 0.9305 (ttt180) cc_final: 0.9016 (tpp80) REVERT: E 52 MET cc_start: 0.8218 (tpt) cc_final: 0.8013 (tpt) REVERT: E 68 PHE cc_start: 0.7659 (m-80) cc_final: 0.7108 (m-10) REVERT: E 105 MET cc_start: 0.9286 (tpt) cc_final: 0.8553 (tpp) REVERT: E 117 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7465 (p0) REVERT: E 210 GLN cc_start: 0.9175 (mt0) cc_final: 0.8695 (mp10) REVERT: E 218 ILE cc_start: 0.8682 (mt) cc_final: 0.8462 (mt) outliers start: 49 outliers final: 41 residues processed: 286 average time/residue: 0.2105 time to fit residues: 84.9685 Evaluate side-chains 294 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10056 Z= 0.269 Angle : 0.895 14.055 13541 Z= 0.434 Chirality : 0.045 0.282 1596 Planarity : 0.004 0.035 1725 Dihedral : 4.284 19.245 1369 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.80 % Allowed : 28.50 % Favored : 66.70 % 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: 1.25 (0.23), residues: 1298 helix: 1.24 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.43 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 18 HIS 0.003 0.001 HIS D 136 PHE 0.032 0.002 PHE F 32 TYR 0.018 0.002 TYR B 237 ARG 0.010 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9206 (tt0) cc_final: 0.8895 (pm20) REVERT: A 195 MET cc_start: 0.9015 (mmm) cc_final: 0.8590 (mtm) REVERT: A 230 ASN cc_start: 0.8892 (t0) cc_final: 0.8317 (p0) REVERT: B 134 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 153 MET cc_start: 0.8584 (tpp) cc_final: 0.7925 (tpp) REVERT: B 210 GLN cc_start: 0.8875 (tt0) cc_final: 0.8319 (pp30) REVERT: B 211 GLU cc_start: 0.8850 (tp30) cc_final: 0.8541 (tp30) REVERT: C 61 ILE cc_start: 0.8795 (tp) cc_final: 0.8196 (tt) REVERT: C 169 MET cc_start: 0.7723 (tmm) cc_final: 0.7510 (tmm) REVERT: C 195 MET cc_start: 0.6210 (mtt) cc_final: 0.5884 (mtt) REVERT: D 28 MET cc_start: 0.7824 (ppp) cc_final: 0.7568 (ptt) REVERT: D 99 GLU cc_start: 0.8554 (mp0) cc_final: 0.8173 (pm20) REVERT: D 105 MET cc_start: 0.8214 (ppp) cc_final: 0.7758 (ppp) REVERT: D 106 GLN cc_start: 0.9068 (mm110) cc_final: 0.8580 (mm-40) REVERT: D 169 MET cc_start: 0.7800 (mmm) cc_final: 0.7569 (mmt) REVERT: D 211 GLU cc_start: 0.8987 (tp30) cc_final: 0.8727 (tp30) REVERT: D 216 ARG cc_start: 0.9292 (ttt180) cc_final: 0.9083 (tpp80) REVERT: E 68 PHE cc_start: 0.7750 (m-80) cc_final: 0.7194 (m-10) REVERT: E 105 MET cc_start: 0.9229 (tpt) cc_final: 0.8578 (tpp) REVERT: E 117 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7389 (p0) REVERT: E 210 GLN cc_start: 0.9183 (mt0) cc_final: 0.8721 (mp10) outliers start: 50 outliers final: 42 residues processed: 280 average time/residue: 0.2321 time to fit residues: 89.9821 Evaluate side-chains 289 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 246 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0040 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.0070 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10056 Z= 0.225 Angle : 0.930 14.313 13541 Z= 0.442 Chirality : 0.045 0.275 1596 Planarity : 0.004 0.038 1725 Dihedral : 4.339 19.659 1369 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.93 % Allowed : 29.08 % Favored : 66.99 % 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: 1.27 (0.23), residues: 1298 helix: 1.26 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.53 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 18 HIS 0.003 0.001 HIS D 136 PHE 0.026 0.001 PHE F 32 TYR 0.019 0.002 TYR B 237 ARG 0.010 0.001 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9186 (tt0) cc_final: 0.8834 (pm20) REVERT: A 75 ASP cc_start: 0.9118 (t0) cc_final: 0.8758 (p0) REVERT: A 195 MET cc_start: 0.8947 (mmm) cc_final: 0.8166 (mtm) REVERT: A 230 ASN cc_start: 0.8843 (t0) cc_final: 0.8266 (p0) REVERT: B 134 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 153 MET cc_start: 0.8548 (tpp) cc_final: 0.7854 (tpp) REVERT: B 194 ASN cc_start: 0.7593 (m-40) cc_final: 0.7364 (m-40) REVERT: C 56 PHE cc_start: 0.7307 (m-80) cc_final: 0.7007 (m-10) REVERT: C 61 ILE cc_start: 0.8808 (tp) cc_final: 0.8595 (tp) REVERT: D 99 GLU cc_start: 0.8556 (mp0) cc_final: 0.8186 (pm20) REVERT: D 105 MET cc_start: 0.8226 (ppp) cc_final: 0.7907 (ppp) REVERT: D 106 GLN cc_start: 0.9060 (mm110) cc_final: 0.8603 (mm-40) REVERT: D 134 GLU cc_start: 0.8343 (pp20) cc_final: 0.7476 (pp20) REVERT: D 211 GLU cc_start: 0.8960 (tp30) cc_final: 0.8695 (tp30) REVERT: E 68 PHE cc_start: 0.7691 (m-80) cc_final: 0.6342 (m-80) REVERT: E 105 MET cc_start: 0.9104 (tpt) cc_final: 0.8518 (tpp) REVERT: E 117 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7460 (p0) REVERT: E 168 ASN cc_start: 0.8094 (m-40) cc_final: 0.7622 (t0) REVERT: E 175 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9201 (tp) REVERT: E 210 GLN cc_start: 0.9188 (mt0) cc_final: 0.8721 (mp10) outliers start: 41 outliers final: 34 residues processed: 293 average time/residue: 0.2130 time to fit residues: 87.8974 Evaluate side-chains 294 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091072 restraints weight = 30013.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093631 restraints weight = 17718.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095300 restraints weight = 12809.172| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10056 Z= 0.260 Angle : 0.950 15.237 13541 Z= 0.458 Chirality : 0.046 0.262 1596 Planarity : 0.004 0.036 1725 Dihedral : 4.350 19.243 1369 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.93 % Allowed : 30.23 % Favored : 65.83 % 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: 1.26 (0.23), residues: 1298 helix: 1.26 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -1.45 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 18 HIS 0.002 0.001 HIS D 136 PHE 0.036 0.002 PHE E 68 TYR 0.018 0.002 TYR B 237 ARG 0.010 0.001 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.54 seconds wall clock time: 45 minutes 49.03 seconds (2749.03 seconds total)