Starting phenix.real_space_refine on Sun Apr 14 15:09:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j05_35884/04_2024/8j05_35884_neut.pdb" } resolution = 2.7 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= 0.003 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 10208 2.51 5 N 2708 2.21 5 O 2872 1.98 5 H 15800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 57": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Time building chain proxies: 13.73, per 1000 atoms: 0.43 Number of scatterers: 31676 At special positions: 0 Unit cell: (126.48, 127.41, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 2872 8.00 N 2708 7.00 C 10208 6.00 H 15800 1.00 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: 25.09 Conformation dependent library (CDL) restraints added in 3.2 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 4 sheets defined 81.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 4.124A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.729A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 329 removed outlier: 3.900A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 538 through 558 Processing helix chain 'A' and resid 562 through 595 removed outlier: 4.604A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.096A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.717A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.620A pdb=" N LYS B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.961A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 329 removed outlier: 3.946A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 538 through 559 Processing helix chain 'B' and resid 564 through 595 Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.787A pdb=" N THR C 80 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.832A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.074A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.703A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.998A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 538 through 558 Processing helix chain 'D' and resid 564 through 595 Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 74 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.988A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.094A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.525A pdb=" N MET F 146 " --> pdb=" O PHE F 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 removed outlier: 4.124A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.705A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.673A pdb=" N MET G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 329 removed outlier: 3.858A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 332 through 350 Processing helix chain 'G' and resid 357 through 367 removed outlier: 3.528A pdb=" N VAL G 367 " --> pdb=" O TYR G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 558 Processing helix chain 'G' and resid 564 through 595 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.879A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.575A pdb=" N ILE F 101 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 137 " --> pdb=" O ILE F 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 1189 hydrogen bonds defined for protein. 3549 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: 11.97 Time building geometry restraints manager: 26.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15772 1.03 - 1.23: 28 1.23 - 1.42: 7000 1.42 - 1.62: 9060 1.62 - 1.81: 148 Bond restraints: 32008 Sorted by residual: bond pdb=" C ARG G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.23e-02 6.61e+03 8.82e-01 bond pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.40e-01 bond pdb=" CB ILE D 205 " pdb=" CG2 ILE D 205 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.63e-01 bond pdb=" CB GLN D 78 " pdb=" CG GLN D 78 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.83e-01 bond pdb=" CB VAL G 320 " pdb=" CG1 VAL G 320 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.25e-01 ... (remaining 32003 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 270 106.43 - 113.34: 36524 113.34 - 120.25: 11578 120.25 - 127.16: 9071 127.16 - 134.08: 141 Bond angle restraints: 57584 Sorted by residual: angle pdb=" N ARG D 213 " pdb=" CA ARG D 213 " pdb=" CB ARG D 213 " ideal model delta sigma weight residual 113.65 110.16 3.49 1.47e+00 4.63e-01 5.62e+00 angle pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " pdb=" CD GLU D 123 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N GLY D 256 " pdb=" CA GLY D 256 " pdb=" C GLY D 256 " ideal model delta sigma weight residual 112.49 115.23 -2.74 1.21e+00 6.83e-01 5.13e+00 angle pdb=" CA TYR G 571 " pdb=" CB TYR G 571 " pdb=" CG TYR G 571 " ideal model delta sigma weight residual 113.90 109.90 4.00 1.80e+00 3.09e-01 4.93e+00 angle pdb=" C ASP F 65 " pdb=" N PHE F 66 " pdb=" CA PHE F 66 " ideal model delta sigma weight residual 119.78 122.50 -2.72 1.24e+00 6.50e-01 4.83e+00 ... (remaining 57579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13113 17.83 - 35.66: 1209 35.66 - 53.49: 459 53.49 - 71.32: 115 71.32 - 89.15: 20 Dihedral angle restraints: 14916 sinusoidal: 7960 harmonic: 6956 Sorted by residual: dihedral pdb=" CA ASP C 57 " pdb=" CB ASP C 57 " pdb=" CG ASP C 57 " pdb=" OD1 ASP C 57 " ideal model delta sinusoidal sigma weight residual -30.00 -89.82 59.82 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG D 89 " pdb=" CD ARG D 89 " pdb=" NE ARG D 89 " pdb=" CZ ARG D 89 " ideal model delta sinusoidal sigma weight residual -90.00 -134.95 44.95 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU E 121 " pdb=" CG GLU E 121 " pdb=" CD GLU E 121 " pdb=" OE1 GLU E 121 " ideal model delta sinusoidal sigma weight residual 0.00 89.15 -89.15 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 14913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1593 0.027 - 0.053: 530 0.053 - 0.080: 196 0.080 - 0.106: 58 0.106 - 0.133: 19 Chirality restraints: 2396 Sorted by residual: chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2393 not shown) Planarity restraints: 4672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 123 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" CD GLU D 123 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D 123 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 123 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 101 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C LEU D 101 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU D 101 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 102 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 100 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C PHE D 100 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE D 100 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 101 " 0.008 2.00e-02 2.50e+03 ... (remaining 4669 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1875 2.18 - 2.79: 64647 2.79 - 3.39: 92053 3.39 - 4.00: 112504 4.00 - 4.60: 176612 Nonbonded interactions: 447691 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" HH TYR D 280 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASP C 57 " pdb=" H GLY C 60 " model vdw 1.580 1.850 nonbonded pdb=" OE2 GLU D 140 " pdb="HH22 ARG D 210 " model vdw 1.590 1.850 nonbonded pdb=" HH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 1.598 1.850 nonbonded pdb=" O LEU B 272 " pdb=" HG1 THR B 276 " model vdw 1.606 1.850 ... (remaining 447686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.420 Extract box with map and model: 4.650 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 98.450 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 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 : 0.003 0.028 16208 Z= 0.172 Angle : 0.470 6.347 21860 Z= 0.264 Chirality : 0.033 0.133 2396 Planarity : 0.003 0.029 2760 Dihedral : 17.085 89.151 5916 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.84 % Allowed : 25.89 % Favored : 73.27 % 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: 2.22 (0.19), residues: 1928 helix: 1.89 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.04 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.006 0.001 HIS A 575 PHE 0.015 0.001 PHE E 90 TYR 0.019 0.001 TYR G 571 ARG 0.002 0.000 ARG G 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 2.517 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 565 MET cc_start: 0.3614 (ppp) cc_final: 0.3247 (ptp) REVERT: B 130 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 72 MET cc_start: -0.1029 (tpt) cc_final: -0.1245 (tpt) REVERT: C 73 MET cc_start: 0.0966 (mmp) cc_final: -0.2881 (tpt) REVERT: C 146 MET cc_start: 0.5845 (tmm) cc_final: 0.4997 (tpt) REVERT: D 87 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7369 (pmt-80) REVERT: D 127 TYR cc_start: 0.7906 (t80) cc_final: 0.7575 (t80) REVERT: D 158 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6552 (mmp80) REVERT: F 73 MET cc_start: 0.0043 (mmt) cc_final: -0.2294 (ttt) REVERT: F 146 MET cc_start: 0.3587 (tpp) cc_final: 0.3287 (tpp) REVERT: G 158 ARG cc_start: 0.6848 (tpt170) cc_final: 0.6504 (mmp80) outliers start: 14 outliers final: 11 residues processed: 180 average time/residue: 2.0195 time to fit residues: 419.8815 Evaluate side-chains 157 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 79 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16208 Z= 0.231 Angle : 0.480 4.998 21860 Z= 0.268 Chirality : 0.034 0.127 2396 Planarity : 0.003 0.055 2760 Dihedral : 4.327 56.862 2195 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 25.30 % Favored : 72.55 % 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: 2.58 (0.19), residues: 1928 helix: 2.15 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.00 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.012 0.001 HIS G 328 PHE 0.020 0.001 PHE E 90 TYR 0.018 0.001 TYR G 571 ARG 0.002 0.000 ARG G 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 2.607 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 168 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6109 (t80) REVERT: A 208 MET cc_start: 0.7124 (tpt) cc_final: 0.6877 (mmm) REVERT: B 166 LYS cc_start: 0.6854 (ttpp) cc_final: 0.6446 (tttm) REVERT: B 168 PHE cc_start: 0.7286 (m-80) cc_final: 0.6108 (t80) REVERT: C 73 MET cc_start: 0.0772 (mmp) cc_final: -0.3025 (tpt) REVERT: C 146 MET cc_start: 0.5755 (tmm) cc_final: 0.4913 (tpt) REVERT: D 127 TYR cc_start: 0.7967 (t80) cc_final: 0.7640 (t80) REVERT: D 168 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6224 (t80) REVERT: E 124 GLU cc_start: -0.0653 (tm-30) cc_final: -0.1063 (tm-30) REVERT: F 84 GLU cc_start: 0.6499 (tt0) cc_final: 0.5605 (mp0) REVERT: F 146 MET cc_start: 0.3941 (tpp) cc_final: 0.3621 (tpp) REVERT: G 158 ARG cc_start: 0.6904 (tpt170) cc_final: 0.6594 (mmm160) outliers start: 36 outliers final: 18 residues processed: 168 average time/residue: 2.1846 time to fit residues: 420.0031 Evaluate side-chains 162 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16208 Z= 0.196 Angle : 0.460 5.429 21860 Z= 0.257 Chirality : 0.033 0.127 2396 Planarity : 0.003 0.044 2760 Dihedral : 3.717 31.623 2176 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.63 % Allowed : 24.05 % Favored : 73.33 % 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: 2.68 (0.19), residues: 1928 helix: 2.25 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.09 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.006 0.001 HIS A 328 PHE 0.014 0.001 PHE E 90 TYR 0.019 0.001 TYR G 571 ARG 0.004 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 2.170 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: A 168 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6127 (t80) REVERT: B 166 LYS cc_start: 0.6851 (ttpp) cc_final: 0.6442 (tttm) REVERT: C 146 MET cc_start: 0.5653 (tmm) cc_final: 0.4749 (tpt) REVERT: D 127 TYR cc_start: 0.7952 (t80) cc_final: 0.7636 (t80) REVERT: D 168 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6272 (t80) REVERT: E 118 THR cc_start: 0.4169 (OUTLIER) cc_final: 0.3860 (t) REVERT: F 84 GLU cc_start: 0.6498 (tt0) cc_final: 0.5612 (mp0) REVERT: F 146 MET cc_start: 0.4178 (tpp) cc_final: 0.3819 (tpp) REVERT: G 158 ARG cc_start: 0.6886 (tpt170) cc_final: 0.6584 (mmm160) outliers start: 44 outliers final: 23 residues processed: 174 average time/residue: 1.9782 time to fit residues: 398.2259 Evaluate side-chains 170 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 GLN G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16208 Z= 0.174 Angle : 0.452 5.670 21860 Z= 0.251 Chirality : 0.033 0.126 2396 Planarity : 0.003 0.041 2760 Dihedral : 3.665 34.831 2176 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.86 % Allowed : 23.75 % Favored : 73.39 % 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: 2.75 (0.19), residues: 1928 helix: 2.32 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.15 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.011 0.001 HIS A 328 PHE 0.018 0.001 PHE E 20 TYR 0.020 0.001 TYR G 571 ARG 0.002 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 2.562 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: A 120 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7451 (tptm) REVERT: A 157 TRP cc_start: 0.5402 (m100) cc_final: 0.5171 (m100) REVERT: A 168 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6118 (t80) REVERT: B 130 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 166 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6369 (tttm) REVERT: C 73 MET cc_start: 0.0515 (mmp) cc_final: -0.3108 (tpt) REVERT: C 142 PHE cc_start: 0.5896 (t80) cc_final: 0.5693 (t80) REVERT: C 146 MET cc_start: 0.5829 (tmm) cc_final: 0.4770 (tpt) REVERT: D 127 TYR cc_start: 0.7935 (t80) cc_final: 0.7621 (t80) REVERT: D 157 TRP cc_start: 0.5083 (m100) cc_final: 0.4670 (m100) REVERT: D 168 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6233 (t80) REVERT: F 84 GLU cc_start: 0.6480 (tt0) cc_final: 0.5595 (mp0) REVERT: F 146 MET cc_start: 0.4271 (tpp) cc_final: 0.3813 (tpp) REVERT: G 133 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7739 (t) REVERT: G 140 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6152 (tt0) REVERT: G 158 ARG cc_start: 0.6750 (tpt170) cc_final: 0.6479 (mmm160) REVERT: G 229 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8739 (p) outliers start: 48 outliers final: 24 residues processed: 179 average time/residue: 2.0683 time to fit residues: 426.8533 Evaluate side-chains 180 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16208 Z= 0.293 Angle : 0.491 5.918 21860 Z= 0.275 Chirality : 0.035 0.132 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.900 55.124 2176 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 24.11 % Favored : 73.15 % 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: 2.51 (0.19), residues: 1928 helix: 2.13 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.011 0.001 HIS A 328 PHE 0.023 0.001 PHE E 20 TYR 0.019 0.002 TYR G 571 ARG 0.003 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 2.381 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: A 120 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7504 (tptm) REVERT: A 158 ARG cc_start: 0.6533 (tpm-80) cc_final: 0.6302 (mmm160) REVERT: A 168 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6395 (t80) REVERT: B 130 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 166 LYS cc_start: 0.6837 (ttpp) cc_final: 0.6398 (tttm) REVERT: C 73 MET cc_start: 0.0655 (mmp) cc_final: -0.3058 (tpt) REVERT: C 140 GLU cc_start: 0.3675 (OUTLIER) cc_final: 0.2814 (mm-30) REVERT: C 146 MET cc_start: 0.5898 (tmm) cc_final: 0.4792 (tpt) REVERT: D 127 TYR cc_start: 0.7945 (t80) cc_final: 0.7615 (t80) REVERT: D 157 TRP cc_start: 0.5210 (m100) cc_final: 0.4794 (m100) REVERT: D 168 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6237 (t80) REVERT: D 289 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: F 84 GLU cc_start: 0.6441 (tt0) cc_final: 0.5533 (mp0) REVERT: F 146 MET cc_start: 0.4265 (tpp) cc_final: 0.3841 (tpp) REVERT: G 133 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7817 (t) REVERT: G 140 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6170 (tt0) REVERT: G 158 ARG cc_start: 0.6834 (tpt170) cc_final: 0.6561 (mmm160) REVERT: G 229 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8805 (p) outliers start: 46 outliers final: 24 residues processed: 172 average time/residue: 2.1566 time to fit residues: 426.2407 Evaluate side-chains 174 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16208 Z= 0.211 Angle : 0.470 5.692 21860 Z= 0.260 Chirality : 0.033 0.127 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.736 49.119 2174 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 24.46 % Favored : 72.97 % 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: 2.60 (0.19), residues: 1928 helix: 2.20 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.19 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.019 0.001 PHE E 90 TYR 0.020 0.001 TYR G 571 ARG 0.002 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 2.462 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 120 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7484 (tptm) REVERT: A 158 ARG cc_start: 0.6528 (tpm-80) cc_final: 0.6271 (mmm160) REVERT: A 168 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6281 (t80) REVERT: A 559 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3383 (tt) REVERT: B 166 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6353 (tttm) REVERT: B 366 THR cc_start: -0.0105 (OUTLIER) cc_final: -0.0346 (m) REVERT: C 73 MET cc_start: 0.0575 (mmp) cc_final: -0.3160 (tpt) REVERT: C 146 MET cc_start: 0.5885 (tmm) cc_final: 0.4884 (tpt) REVERT: D 127 TYR cc_start: 0.7924 (t80) cc_final: 0.7535 (t80) REVERT: D 157 TRP cc_start: 0.5252 (m100) cc_final: 0.4860 (m100) REVERT: D 168 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6241 (t80) REVERT: D 560 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.4459 (mtm-85) REVERT: F 84 GLU cc_start: 0.6445 (tt0) cc_final: 0.5537 (mp0) REVERT: F 146 MET cc_start: 0.4269 (tpp) cc_final: 0.3863 (tpp) REVERT: G 70 ARG cc_start: 0.3921 (ptt90) cc_final: 0.3689 (ptm-80) REVERT: G 140 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: G 158 ARG cc_start: 0.6803 (tpt170) cc_final: 0.6528 (mmm160) REVERT: G 229 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8775 (p) REVERT: G 330 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: H 146 MET cc_start: 0.6343 (mmt) cc_final: 0.6065 (tpt) outliers start: 43 outliers final: 25 residues processed: 170 average time/residue: 2.2785 time to fit residues: 442.6822 Evaluate side-chains 177 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 GLN G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16208 Z= 0.269 Angle : 0.486 5.734 21860 Z= 0.270 Chirality : 0.034 0.127 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.682 23.099 2174 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 24.34 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.19), residues: 1928 helix: 2.12 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.21 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.019 0.001 PHE E 90 TYR 0.019 0.002 TYR G 571 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 142 time to evaluate : 2.227 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 120 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7499 (tptm) REVERT: A 158 ARG cc_start: 0.6527 (tpm-80) cc_final: 0.6242 (mmm160) REVERT: A 168 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 559 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3461 (tt) REVERT: B 130 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 166 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6442 (tttm) REVERT: B 366 THR cc_start: -0.0026 (OUTLIER) cc_final: -0.0288 (m) REVERT: C 146 MET cc_start: 0.5865 (tmm) cc_final: 0.4846 (tpt) REVERT: D 127 TYR cc_start: 0.7942 (t80) cc_final: 0.7611 (t80) REVERT: D 157 TRP cc_start: 0.5234 (m100) cc_final: 0.4849 (m100) REVERT: D 289 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7802 (m-40) REVERT: D 327 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7296 (pptt) REVERT: D 560 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4422 (mtm-85) REVERT: F 84 GLU cc_start: 0.6513 (tt0) cc_final: 0.5599 (mp0) REVERT: F 146 MET cc_start: 0.4321 (tpp) cc_final: 0.3912 (tpp) REVERT: G 70 ARG cc_start: 0.3890 (ptt90) cc_final: 0.3667 (ptm-80) REVERT: G 120 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7524 (tptm) REVERT: G 133 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (t) REVERT: G 140 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6189 (tt0) REVERT: G 158 ARG cc_start: 0.6794 (tpt170) cc_final: 0.6513 (mmm160) REVERT: G 229 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8811 (p) outliers start: 50 outliers final: 25 residues processed: 175 average time/residue: 2.3556 time to fit residues: 468.0947 Evaluate side-chains 177 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16208 Z= 0.276 Angle : 0.493 5.908 21860 Z= 0.274 Chirality : 0.035 0.127 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.671 17.580 2172 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.63 % Allowed : 24.94 % Favored : 72.43 % 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: 2.42 (0.19), residues: 1928 helix: 2.07 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.017 0.001 PHE E 90 TYR 0.020 0.002 TYR G 571 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 2.688 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 120 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7503 (tptm) REVERT: A 158 ARG cc_start: 0.6468 (tpm-80) cc_final: 0.6176 (mmm160) REVERT: A 168 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6383 (t80) REVERT: A 559 LEU cc_start: 0.3585 (OUTLIER) cc_final: 0.3326 (tt) REVERT: B 130 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 166 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6474 (tttm) REVERT: B 366 THR cc_start: 0.0016 (OUTLIER) cc_final: -0.0246 (m) REVERT: C 146 MET cc_start: 0.5910 (tmm) cc_final: 0.4840 (tpt) REVERT: D 127 TYR cc_start: 0.7939 (t80) cc_final: 0.7593 (t80) REVERT: D 157 TRP cc_start: 0.5151 (m100) cc_final: 0.4781 (m100) REVERT: F 84 GLU cc_start: 0.6547 (tt0) cc_final: 0.5623 (mp0) REVERT: F 146 MET cc_start: 0.4332 (tpp) cc_final: 0.3956 (tpp) REVERT: G 70 ARG cc_start: 0.3881 (ptt90) cc_final: 0.3657 (ptm-80) REVERT: G 120 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7530 (tptm) REVERT: G 133 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7774 (t) REVERT: G 140 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: G 229 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8810 (p) outliers start: 44 outliers final: 27 residues processed: 163 average time/residue: 2.2662 time to fit residues: 421.3425 Evaluate side-chains 171 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16208 Z= 0.213 Angle : 0.478 6.904 21860 Z= 0.264 Chirality : 0.033 0.126 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.618 16.974 2172 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.68 % Allowed : 25.18 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1928 helix: 2.17 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.017 0.001 PHE E 90 TYR 0.020 0.001 TYR G 571 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 2.300 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: A 120 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7482 (tptm) REVERT: A 133 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7856 (t) REVERT: A 158 ARG cc_start: 0.6473 (tpm-80) cc_final: 0.6178 (mmm160) REVERT: A 168 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 559 LEU cc_start: 0.3673 (OUTLIER) cc_final: 0.3407 (tt) REVERT: B 130 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 166 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6446 (tttm) REVERT: B 366 THR cc_start: -0.0001 (OUTLIER) cc_final: -0.0260 (m) REVERT: C 73 MET cc_start: 0.0940 (mmp) cc_final: -0.2756 (tpt) REVERT: C 146 MET cc_start: 0.5886 (tmm) cc_final: 0.4842 (tpt) REVERT: D 127 TYR cc_start: 0.7922 (t80) cc_final: 0.7521 (t80) REVERT: D 157 TRP cc_start: 0.5203 (m100) cc_final: 0.4817 (m100) REVERT: D 327 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7312 (pptt) REVERT: F 84 GLU cc_start: 0.6538 (tt0) cc_final: 0.5622 (mp0) REVERT: F 146 MET cc_start: 0.4283 (tpp) cc_final: 0.3892 (tpp) REVERT: G 70 ARG cc_start: 0.3878 (ptt90) cc_final: 0.3650 (ptm-80) REVERT: G 120 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7507 (tptm) REVERT: G 133 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7811 (t) REVERT: G 229 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8781 (p) outliers start: 45 outliers final: 28 residues processed: 165 average time/residue: 2.2528 time to fit residues: 424.3047 Evaluate side-chains 170 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 191 optimal weight: 30.0000 chunk 176 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16208 Z= 0.220 Angle : 0.480 7.508 21860 Z= 0.266 Chirality : 0.033 0.126 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.604 16.383 2172 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.39 % Allowed : 25.72 % Favored : 71.90 % 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: 2.59 (0.19), residues: 1928 helix: 2.19 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.017 0.001 PHE E 90 TYR 0.019 0.001 TYR G 571 ARG 0.003 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 2.686 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: A 120 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7481 (tptm) REVERT: A 123 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 133 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (t) REVERT: A 158 ARG cc_start: 0.6474 (tpm-80) cc_final: 0.6187 (mmm160) REVERT: A 168 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6345 (t80) REVERT: A 559 LEU cc_start: 0.3547 (OUTLIER) cc_final: 0.3282 (tt) REVERT: B 123 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: B 130 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 166 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6457 (tttm) REVERT: B 366 THR cc_start: -0.0023 (OUTLIER) cc_final: -0.0281 (m) REVERT: C 73 MET cc_start: 0.1004 (mmp) cc_final: -0.2599 (tpt) REVERT: C 146 MET cc_start: 0.5872 (tmm) cc_final: 0.4830 (tpt) REVERT: D 127 TYR cc_start: 0.7920 (t80) cc_final: 0.7526 (t80) REVERT: D 157 TRP cc_start: 0.5140 (m100) cc_final: 0.4782 (m100) REVERT: D 327 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7311 (pptt) REVERT: F 84 GLU cc_start: 0.6528 (tt0) cc_final: 0.5603 (mp0) REVERT: F 146 MET cc_start: 0.4199 (tpp) cc_final: 0.3748 (tpp) REVERT: G 70 ARG cc_start: 0.3879 (ptt90) cc_final: 0.3649 (ptm-80) REVERT: G 120 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7491 (tptm) REVERT: G 133 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7781 (t) REVERT: G 229 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8779 (p) outliers start: 40 outliers final: 25 residues processed: 160 average time/residue: 2.2899 time to fit residues: 422.2911 Evaluate side-chains 171 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.252334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146074 restraints weight = 54826.114| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.13 r_work: 0.3356 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16208 Z= 0.395 Angle : 0.549 8.367 21860 Z= 0.305 Chirality : 0.038 0.148 2396 Planarity : 0.004 0.038 2760 Dihedral : 3.859 18.084 2172 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.45 % Allowed : 25.89 % Favored : 71.66 % 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: 2.08 (0.19), residues: 1928 helix: 1.81 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 344 HIS 0.011 0.002 HIS A 328 PHE 0.019 0.002 PHE A 168 TYR 0.022 0.002 TYR A 74 ARG 0.004 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9871.34 seconds wall clock time: 176 minutes 6.14 seconds (10566.14 seconds total)