Starting phenix.real_space_refine on Thu Jun 27 10:59:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9z_39873/06_2024/8z9z_39873_updated.pdb" } resolution = 3.5 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= 0.007 sd= 0.091 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 P 6 5.49 5 S 69 5.16 5 C 8436 2.51 5 N 1935 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 6": "OD1" <-> "OD2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 6": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 287": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12648 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3140 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2600 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.51 Number of scatterers: 12648 At special positions: 0 Unit cell: (115.56, 121.98, 130.54, 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 69 16.00 P 6 15.00 O 2202 8.00 N 1935 7.00 C 8436 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: 4.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 2 sheets defined 75.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 8 through 11 No H-bonds generated for 'chain 'A' and resid 8 through 11' Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 35 through 63 removed outlier: 3.815A pdb=" N MET A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 removed outlier: 3.829A pdb=" N HIS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 117 through 155 removed outlier: 3.886A pdb=" N THR A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 245 removed outlier: 3.933A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.953A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 335 Processing helix chain 'A' and resid 338 through 360 removed outlier: 3.839A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 404 removed outlier: 3.606A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 442 through 462 Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 70 through 94 removed outlier: 3.766A pdb=" N HIS B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 114 through 154 removed outlier: 3.734A pdb=" N ALA B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 152 " --> pdb=" O TRP B 149 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 245 removed outlier: 3.580A pdb=" N MET B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 4.040A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 335 Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.848A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 404 removed outlier: 4.001A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 442 through 462 Processing helix chain 'C' and resid 8 through 11 No H-bonds generated for 'chain 'C' and resid 8 through 11' Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 37 through 66 Processing helix chain 'C' and resid 70 through 95 removed outlier: 3.857A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 117 through 151 removed outlier: 3.694A pdb=" N THR C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 193 through 245 removed outlier: 3.613A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.644A pdb=" N GLU C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 335 Processing helix chain 'C' and resid 338 through 359 removed outlier: 3.594A pdb=" N VAL C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 405 removed outlier: 3.546A pdb=" N ILE C 382 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N MET C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 426 Processing helix chain 'C' and resid 442 through 462 Processing helix chain 'D' and resid 7 through 14 Processing helix chain 'D' and resid 21 through 41 Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 51 through 88 removed outlier: 3.555A pdb=" N PHE D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 116 removed outlier: 3.580A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 201 removed outlier: 4.038A pdb=" N ILE D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 185 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 252 removed outlier: 4.925A pdb=" N LYS D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 263 through 299 removed outlier: 5.055A pdb=" N SER D 270 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 284 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU D 287 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 291 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS D 292 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 338 through 359 Processing sheet with id= A, first strand: chain 'A' and resid 159 through 163 Processing sheet with id= B, first strand: chain 'B' and resid 159 through 163 870 hydrogen bonds defined for protein. 2430 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: 3.62 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2022 1.33 - 1.45: 3677 1.45 - 1.57: 7153 1.57 - 1.69: 12 1.69 - 1.82: 112 Bond restraints: 12976 Sorted by residual: bond pdb=" CB GLU D 205 " pdb=" CG GLU D 205 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" CA PHE A 62 " pdb=" CB PHE A 62 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.25e+00 bond pdb=" SD MET D 13 " pdb=" CE MET D 13 " ideal model delta sigma weight residual 1.791 1.766 0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" CB GLU D 287 " pdb=" CG GLU D 287 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CB PHE C 90 " pdb=" CG PHE C 90 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.36e-01 ... (remaining 12971 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.85: 178 105.85 - 112.94: 7151 112.94 - 120.03: 4546 120.03 - 127.11: 5553 127.11 - 134.20: 143 Bond angle restraints: 17571 Sorted by residual: angle pdb=" CB MET D 84 " pdb=" CG MET D 84 " pdb=" SD MET D 84 " ideal model delta sigma weight residual 112.70 104.19 8.51 3.00e+00 1.11e-01 8.05e+00 angle pdb=" CA CYS A 426 " pdb=" CB CYS A 426 " pdb=" SG CYS A 426 " ideal model delta sigma weight residual 114.40 120.76 -6.36 2.30e+00 1.89e-01 7.65e+00 angle pdb=" CA GLN A 425 " pdb=" CB GLN A 425 " pdb=" CG GLN A 425 " ideal model delta sigma weight residual 114.10 108.59 5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" CA CYS A 426 " pdb=" C CYS A 426 " pdb=" O CYS A 426 " ideal model delta sigma weight residual 120.51 124.39 -3.88 1.43e+00 4.89e-01 7.38e+00 angle pdb=" CB GLU D 287 " pdb=" CG GLU D 287 " pdb=" CD GLU D 287 " ideal model delta sigma weight residual 112.60 117.14 -4.54 1.70e+00 3.46e-01 7.13e+00 ... (remaining 17566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6334 17.97 - 35.93: 945 35.93 - 53.90: 247 53.90 - 71.86: 46 71.86 - 89.83: 15 Dihedral angle restraints: 7587 sinusoidal: 3076 harmonic: 4511 Sorted by residual: dihedral pdb=" CA ASN C 214 " pdb=" CB ASN C 214 " pdb=" CG ASN C 214 " pdb=" OD1 ASN C 214 " ideal model delta sinusoidal sigma weight residual -90.00 -162.03 72.03 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG D 90 " pdb=" CD ARG D 90 " pdb=" NE ARG D 90 " pdb=" CZ ARG D 90 " ideal model delta sinusoidal sigma weight residual -90.00 -134.94 44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU D 64 " pdb=" CG GLU D 64 " pdb=" CD GLU D 64 " pdb=" OE1 GLU D 64 " ideal model delta sinusoidal sigma weight residual 0.00 -89.83 89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1682 0.050 - 0.100: 303 0.100 - 0.149: 25 0.149 - 0.199: 2 0.199 - 0.249: 1 Chirality restraints: 2013 Sorted by residual: chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE D 242 " pdb=" CA ILE D 242 " pdb=" CG1 ILE D 242 " pdb=" CG2 ILE D 242 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 2010 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 176 " 0.041 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 177 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 456 " -0.013 2.00e-02 2.50e+03 1.55e-02 4.23e+00 pdb=" CG PHE C 456 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 456 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 456 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 456 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 456 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 408 " 0.012 2.00e-02 2.50e+03 1.20e-02 3.61e+00 pdb=" CG TRP B 408 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 408 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 408 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 408 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 408 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 408 " -0.000 2.00e-02 2.50e+03 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1500 2.75 - 3.29: 12743 3.29 - 3.82: 22422 3.82 - 4.36: 23162 4.36 - 4.90: 42219 Nonbonded interactions: 102046 Sorted by model distance: nonbonded pdb=" O ILE D 266 " pdb=" OG SER D 270 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR B 142 " pdb=" OD1 ASN B 214 " model vdw 2.217 2.440 nonbonded pdb=" OG SER D 230 " pdb=" O12 PC1 D 401 " model vdw 2.225 2.440 nonbonded pdb=" NE2 GLN A 420 " pdb=" OE1 GLN A 424 " model vdw 2.252 2.520 nonbonded pdb=" OG1 THR A 142 " pdb=" OD1 ASN A 214 " model vdw 2.260 2.440 ... (remaining 102041 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 5 through 156 or resid 175 through 463 or resid 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = chain 'C' } 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 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.340 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.630 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.002 0.034 12976 Z= 0.151 Angle : 0.481 8.511 17571 Z= 0.255 Chirality : 0.036 0.249 2013 Planarity : 0.003 0.063 2079 Dihedral : 18.144 89.830 4667 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.29 % Allowed : 29.95 % Favored : 69.76 % 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: 3.18 (0.22), residues: 1501 helix: 2.98 (0.15), residues: 1165 sheet: -0.02 (1.23), residues: 24 loop : -1.36 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 408 HIS 0.003 0.001 HIS D 85 PHE 0.036 0.001 PHE C 456 TYR 0.018 0.001 TYR D 243 ARG 0.002 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 391 GLU cc_start: 0.7976 (tt0) cc_final: 0.7701 (tt0) REVERT: C 328 TYR cc_start: 0.8320 (t80) cc_final: 0.7976 (t80) REVERT: D 13 MET cc_start: 0.7250 (mtm) cc_final: 0.6569 (mtm) REVERT: D 239 PHE cc_start: 0.7804 (t80) cc_final: 0.7600 (t80) REVERT: D 243 TYR cc_start: 0.6801 (m-10) cc_final: 0.6508 (m-10) outliers start: 4 outliers final: 1 residues processed: 201 average time/residue: 0.1912 time to fit residues: 59.6855 Evaluate side-chains 193 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 0.0370 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12976 Z= 0.175 Angle : 0.444 7.752 17571 Z= 0.238 Chirality : 0.035 0.172 2013 Planarity : 0.004 0.062 2079 Dihedral : 9.704 77.049 1919 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.27 % Favored : 69.83 % 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: 2.95 (0.22), residues: 1501 helix: 2.79 (0.15), residues: 1166 sheet: 0.07 (1.22), residues: 24 loop : -1.39 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 408 HIS 0.002 0.001 HIS B 388 PHE 0.020 0.001 PHE D 173 TYR 0.012 0.001 TYR D 243 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 GLU cc_start: 0.8024 (tt0) cc_final: 0.7740 (tt0) REVERT: C 328 TYR cc_start: 0.8383 (t80) cc_final: 0.7971 (t80) REVERT: D 47 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6348 (t80) REVERT: D 54 GLN cc_start: 0.5324 (OUTLIER) cc_final: 0.4935 (mp10) REVERT: D 78 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8012 (ttmt) REVERT: D 352 LEU cc_start: 0.8610 (mm) cc_final: 0.8376 (mt) outliers start: 40 outliers final: 25 residues processed: 234 average time/residue: 0.1930 time to fit residues: 69.7246 Evaluate side-chains 227 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN D 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12976 Z= 0.255 Angle : 0.483 7.870 17571 Z= 0.254 Chirality : 0.037 0.207 2013 Planarity : 0.004 0.064 2079 Dihedral : 9.670 76.237 1917 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.71 % Allowed : 26.76 % Favored : 68.53 % 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: 2.66 (0.22), residues: 1501 helix: 2.57 (0.15), residues: 1167 sheet: 0.15 (1.22), residues: 24 loop : -1.45 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 408 HIS 0.004 0.001 HIS B 388 PHE 0.019 0.001 PHE C 90 TYR 0.010 0.001 TYR B 92 ARG 0.001 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 202 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8381 (t80) cc_final: 0.8017 (t80) REVERT: C 328 TYR cc_start: 0.8510 (t80) cc_final: 0.8139 (t80) REVERT: D 13 MET cc_start: 0.7547 (mtm) cc_final: 0.6830 (tmm) REVERT: D 47 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6575 (t80) REVERT: D 166 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 173 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6929 (t80) REVERT: D 340 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7363 (tt) REVERT: D 352 LEU cc_start: 0.8573 (mm) cc_final: 0.8351 (mt) outliers start: 65 outliers final: 47 residues processed: 241 average time/residue: 0.1957 time to fit residues: 72.0156 Evaluate side-chains 243 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 64 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12976 Z= 0.153 Angle : 0.431 7.624 17571 Z= 0.229 Chirality : 0.035 0.209 2013 Planarity : 0.004 0.062 2079 Dihedral : 9.489 75.157 1917 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.26 % Allowed : 28.28 % Favored : 68.46 % 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: 2.81 (0.22), residues: 1501 helix: 2.70 (0.15), residues: 1163 sheet: 0.07 (1.21), residues: 24 loop : -1.45 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 408 HIS 0.009 0.001 HIS D 108 PHE 0.027 0.001 PHE D 73 TYR 0.012 0.001 TYR D 165 ARG 0.001 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8409 (t80) cc_final: 0.8015 (t80) REVERT: B 391 GLU cc_start: 0.8073 (tt0) cc_final: 0.7805 (tt0) REVERT: C 328 TYR cc_start: 0.8411 (t80) cc_final: 0.8034 (t80) REVERT: D 13 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6775 (tmm) REVERT: D 27 TYR cc_start: 0.4719 (OUTLIER) cc_final: 0.2742 (m-80) REVERT: D 54 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5515 (mp10) REVERT: D 165 TYR cc_start: 0.7469 (p90) cc_final: 0.7259 (p90) REVERT: D 173 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6876 (t80) outliers start: 45 outliers final: 28 residues processed: 236 average time/residue: 0.1893 time to fit residues: 69.7112 Evaluate side-chains 231 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12976 Z= 0.282 Angle : 0.509 8.278 17571 Z= 0.268 Chirality : 0.038 0.216 2013 Planarity : 0.004 0.064 2079 Dihedral : 9.717 76.399 1917 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.64 % Allowed : 27.34 % Favored : 68.02 % 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: 2.54 (0.22), residues: 1501 helix: 2.50 (0.15), residues: 1164 sheet: 0.10 (1.21), residues: 24 loop : -1.51 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 408 HIS 0.004 0.001 HIS B 226 PHE 0.017 0.001 PHE C 90 TYR 0.010 0.001 TYR D 165 ARG 0.002 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8076 (mmm) cc_final: 0.7761 (mmp) REVERT: A 334 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: A 455 TYR cc_start: 0.8428 (t80) cc_final: 0.8055 (t80) REVERT: C 328 TYR cc_start: 0.8577 (t80) cc_final: 0.8202 (t80) REVERT: D 13 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6566 (tmm) REVERT: D 27 TYR cc_start: 0.4765 (OUTLIER) cc_final: 0.2859 (m-80) REVERT: D 54 GLN cc_start: 0.5843 (OUTLIER) cc_final: 0.5492 (mp10) REVERT: D 173 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7166 (t80) outliers start: 64 outliers final: 45 residues processed: 237 average time/residue: 0.1817 time to fit residues: 67.6702 Evaluate side-chains 240 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12976 Z= 0.145 Angle : 0.435 7.853 17571 Z= 0.230 Chirality : 0.035 0.215 2013 Planarity : 0.004 0.062 2079 Dihedral : 9.394 75.360 1917 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.12 % Allowed : 28.79 % Favored : 68.09 % 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 (0.22), residues: 1501 helix: 2.70 (0.15), residues: 1158 sheet: 0.12 (1.22), residues: 24 loop : -1.56 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 408 HIS 0.002 0.000 HIS D 108 PHE 0.027 0.001 PHE D 73 TYR 0.017 0.001 TYR D 221 ARG 0.001 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8418 (t80) cc_final: 0.8018 (t80) REVERT: C 328 TYR cc_start: 0.8400 (t80) cc_final: 0.7841 (t80) REVERT: C 420 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: C 449 LEU cc_start: 0.8612 (tp) cc_final: 0.8374 (tp) REVERT: D 13 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6708 (tmm) REVERT: D 27 TYR cc_start: 0.4786 (OUTLIER) cc_final: 0.2827 (m-80) REVERT: D 54 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5432 (mp10) REVERT: D 250 PHE cc_start: 0.6378 (t80) cc_final: 0.6003 (t80) outliers start: 43 outliers final: 29 residues processed: 231 average time/residue: 0.2012 time to fit residues: 72.0499 Evaluate side-chains 226 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12976 Z= 0.186 Angle : 0.468 8.774 17571 Z= 0.245 Chirality : 0.036 0.222 2013 Planarity : 0.004 0.061 2079 Dihedral : 9.376 75.732 1917 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.48 % Allowed : 28.64 % Favored : 67.88 % 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: 2.73 (0.22), residues: 1501 helix: 2.68 (0.15), residues: 1157 sheet: 0.16 (1.22), residues: 24 loop : -1.55 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.016 0.001 PHE C 90 TYR 0.019 0.001 TYR A 101 ARG 0.003 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8411 (t80) cc_final: 0.8003 (t80) REVERT: C 328 TYR cc_start: 0.8409 (t80) cc_final: 0.8002 (t80) REVERT: C 409 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7351 (p90) REVERT: C 449 LEU cc_start: 0.8621 (tp) cc_final: 0.8406 (tp) REVERT: D 10 PHE cc_start: 0.7567 (t80) cc_final: 0.5777 (p90) REVERT: D 13 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: D 27 TYR cc_start: 0.4661 (OUTLIER) cc_final: 0.2805 (m-80) REVERT: D 54 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5468 (mp10) REVERT: D 78 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8019 (ttmt) REVERT: D 250 PHE cc_start: 0.6276 (t80) cc_final: 0.6014 (t80) REVERT: D 352 LEU cc_start: 0.8519 (mm) cc_final: 0.8230 (mt) outliers start: 48 outliers final: 38 residues processed: 230 average time/residue: 0.1898 time to fit residues: 67.8484 Evaluate side-chains 237 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12976 Z= 0.168 Angle : 0.453 7.989 17571 Z= 0.236 Chirality : 0.036 0.233 2013 Planarity : 0.004 0.061 2079 Dihedral : 9.304 76.017 1917 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.48 % Allowed : 28.93 % Favored : 67.59 % 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: 2.71 (0.22), residues: 1501 helix: 2.66 (0.15), residues: 1157 sheet: 0.15 (1.22), residues: 24 loop : -1.54 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 408 HIS 0.002 0.001 HIS B 322 PHE 0.026 0.001 PHE D 73 TYR 0.016 0.001 TYR A 101 ARG 0.001 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7488 (pmm) cc_final: 0.7278 (pmm) REVERT: A 455 TYR cc_start: 0.8410 (t80) cc_final: 0.8060 (t80) REVERT: C 328 TYR cc_start: 0.8406 (t80) cc_final: 0.8010 (t80) REVERT: C 409 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7435 (p90) REVERT: C 449 LEU cc_start: 0.8615 (tp) cc_final: 0.8401 (tp) REVERT: D 13 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6824 (tmm) REVERT: D 27 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.2816 (m-80) REVERT: D 54 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5452 (mp10) REVERT: D 78 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8030 (ttmt) REVERT: D 250 PHE cc_start: 0.6272 (t80) cc_final: 0.5910 (t80) REVERT: D 352 LEU cc_start: 0.8509 (mm) cc_final: 0.8215 (mt) outliers start: 48 outliers final: 41 residues processed: 235 average time/residue: 0.1872 time to fit residues: 68.8319 Evaluate side-chains 243 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12976 Z= 0.244 Angle : 0.507 10.104 17571 Z= 0.264 Chirality : 0.037 0.235 2013 Planarity : 0.004 0.061 2079 Dihedral : 9.435 77.053 1917 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.70 % Allowed : 28.86 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.22), residues: 1501 helix: 2.54 (0.15), residues: 1158 sheet: 0.18 (1.22), residues: 24 loop : -1.56 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 408 HIS 0.004 0.001 HIS B 322 PHE 0.018 0.001 PHE C 90 TYR 0.009 0.001 TYR D 165 ARG 0.002 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8441 (t80) cc_final: 0.8081 (t80) REVERT: B 179 LEU cc_start: 0.8762 (mm) cc_final: 0.8538 (mm) REVERT: C 328 TYR cc_start: 0.8491 (t80) cc_final: 0.8085 (t80) REVERT: C 409 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7366 (p90) REVERT: C 449 LEU cc_start: 0.8636 (tp) cc_final: 0.8418 (tp) REVERT: D 13 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7468 (mtt) REVERT: D 27 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.2974 (m-80) REVERT: D 54 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.5448 (mp10) REVERT: D 173 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7041 (t80) REVERT: D 250 PHE cc_start: 0.6253 (t80) cc_final: 0.5986 (t80) REVERT: D 352 LEU cc_start: 0.8504 (mm) cc_final: 0.8216 (mt) outliers start: 51 outliers final: 41 residues processed: 233 average time/residue: 0.1849 time to fit residues: 66.9917 Evaluate side-chains 242 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 148 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12976 Z= 0.183 Angle : 0.472 8.804 17571 Z= 0.246 Chirality : 0.036 0.242 2013 Planarity : 0.004 0.061 2079 Dihedral : 9.334 77.235 1917 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.55 % Allowed : 28.93 % Favored : 67.51 % 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: 2.61 (0.22), residues: 1501 helix: 2.58 (0.15), residues: 1158 sheet: 0.27 (1.23), residues: 24 loop : -1.55 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.029 0.001 PHE C 456 TYR 0.010 0.001 TYR D 165 ARG 0.001 0.000 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8479 (m-80) cc_final: 0.8224 (m-80) REVERT: A 455 TYR cc_start: 0.8437 (t80) cc_final: 0.8070 (t80) REVERT: B 172 MET cc_start: 0.8100 (mpp) cc_final: 0.7683 (mtm) REVERT: C 328 TYR cc_start: 0.8407 (t80) cc_final: 0.7863 (t80) REVERT: C 409 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7435 (p90) REVERT: C 449 LEU cc_start: 0.8614 (tp) cc_final: 0.8403 (tp) REVERT: D 13 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6750 (tmm) REVERT: D 27 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.3077 (m-80) REVERT: D 54 GLN cc_start: 0.5718 (OUTLIER) cc_final: 0.5351 (mp10) REVERT: D 173 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6834 (t80) REVERT: D 250 PHE cc_start: 0.6095 (t80) cc_final: 0.5825 (t80) outliers start: 49 outliers final: 41 residues processed: 232 average time/residue: 0.1842 time to fit residues: 66.8931 Evaluate side-chains 244 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 400 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138585 restraints weight = 15315.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136896 restraints weight = 12810.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137743 restraints weight = 10946.214| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12976 Z= 0.202 Angle : 0.490 8.697 17571 Z= 0.255 Chirality : 0.036 0.239 2013 Planarity : 0.004 0.061 2079 Dihedral : 9.349 77.552 1917 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.77 % Allowed : 29.01 % Favored : 67.22 % 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 (0.22), residues: 1501 helix: 2.57 (0.15), residues: 1158 sheet: 0.37 (1.22), residues: 24 loop : -1.57 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.019 0.001 PHE C 90 TYR 0.010 0.001 TYR D 165 ARG 0.004 0.000 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.37 seconds wall clock time: 40 minutes 39.66 seconds (2439.66 seconds total)