Starting phenix.real_space_refine on Thu Feb 15 01:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kaq_22780/02_2024/7kaq_22780.pdb" } resolution = 4.0 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= 0.008 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 7008 2.51 5 N 1812 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 472": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D GLU 559": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10753 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3345 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3864 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 28, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 6.05, per 1000 atoms: 0.56 Number of scatterers: 10753 At special positions: 0 Unit cell: (108.1, 125.35, 135.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1894 8.00 N 1812 7.00 C 7008 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: 4.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 71.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.651A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.838A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.946A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.560A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.722A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.696A pdb=" N THR A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.576A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.588A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 65 removed outlier: 4.239A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.777A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.645A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.855A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.325A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.756A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.066A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 removed outlier: 3.517A pdb=" N LEU D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.606A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.079A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 486 removed outlier: 4.248A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.590A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 545 removed outlier: 6.777A pdb=" N ASP D 542 " --> pdb=" O ASN D 539 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP D 543 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 544 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 545 " --> pdb=" O ASP D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.534A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.595A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 123 Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.513A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.513A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.123A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.589A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 41 Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.808A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.631A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 3.619A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.640A pdb=" N UNK G 170 " --> pdb=" O UNK G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 6.805A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 435 " --> pdb=" O TYR D 450 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR D 450 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 705 hydrogen bonds defined for protein. 2070 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: 3.00 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: 1.23 - 1.34: 3404 1.34 - 1.46: 2126 1.46 - 1.57: 5370 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10961 Sorted by residual: bond pdb=" C LYS D 493 " pdb=" N GLN D 494 " ideal model delta sigma weight residual 1.331 1.305 0.026 2.83e-02 1.25e+03 8.58e-01 bond pdb=" CA LEU F 102 " pdb=" C LEU F 102 " ideal model delta sigma weight residual 1.521 1.529 -0.008 1.14e-02 7.69e+03 5.47e-01 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.27e-01 bond pdb=" C GLU D 12 " pdb=" N THR D 13 " ideal model delta sigma weight residual 1.332 1.322 0.010 1.40e-02 5.10e+03 5.27e-01 bond pdb=" CB VAL C 54 " pdb=" CG1 VAL C 54 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.09e-01 ... (remaining 10956 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 303 106.98 - 113.73: 6368 113.73 - 120.49: 4298 120.49 - 127.24: 3797 127.24 - 134.00: 107 Bond angle restraints: 14873 Sorted by residual: angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.11e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.55 114.48 -3.93 1.63e+00 3.76e-01 5.80e+00 angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 114.00 110.93 3.07 1.31e+00 5.83e-01 5.48e+00 angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 111.81 109.93 1.88 8.60e-01 1.35e+00 4.79e+00 angle pdb=" C PRO D 471 " pdb=" N GLU D 472 " pdb=" CA GLU D 472 " ideal model delta sigma weight residual 121.54 125.52 -3.98 1.91e+00 2.74e-01 4.35e+00 ... (remaining 14868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6189 17.67 - 35.33: 338 35.33 - 53.00: 54 53.00 - 70.67: 5 70.67 - 88.33: 9 Dihedral angle restraints: 6595 sinusoidal: 2518 harmonic: 4077 Sorted by residual: dihedral pdb=" CA SER A 289 " pdb=" C SER A 289 " pdb=" N ASN A 290 " pdb=" CA ASN A 290 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU E 144 " pdb=" CG GLU E 144 " pdb=" CD GLU E 144 " pdb=" OE1 GLU E 144 " ideal model delta sinusoidal sigma weight residual 0.00 -88.33 88.33 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " pdb=" OE1 GLU F 63 " ideal model delta sinusoidal sigma weight residual 0.00 -88.00 88.00 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1075 0.027 - 0.054: 452 0.054 - 0.080: 160 0.080 - 0.107: 78 0.107 - 0.134: 12 Chirality restraints: 1777 Sorted by residual: chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CB THR D 448 " pdb=" CA THR D 448 " pdb=" OG1 THR D 448 " pdb=" CG2 THR D 448 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA SER A 83 " pdb=" N SER A 83 " pdb=" C SER A 83 " pdb=" CB SER A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1774 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO F 48 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 463 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO F 94 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.014 5.00e-02 4.00e+02 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 287 2.71 - 3.25: 11487 3.25 - 3.80: 17396 3.80 - 4.35: 20289 4.35 - 4.90: 34815 Nonbonded interactions: 84274 Sorted by model distance: nonbonded pdb=" OH TYR A 287 " pdb=" OG1 THR A 386 " model vdw 2.158 2.440 nonbonded pdb=" OG SER A 72 " pdb=" O LEU A 78 " model vdw 2.214 2.440 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.242 2.520 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.247 2.440 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.252 2.440 ... (remaining 84269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 4.090 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 31.530 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.026 10961 Z= 0.167 Angle : 0.521 9.533 14873 Z= 0.290 Chirality : 0.037 0.134 1777 Planarity : 0.003 0.041 1855 Dihedral : 11.528 88.332 3945 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1322 helix: 0.29 (0.17), residues: 833 sheet: -2.85 (0.44), residues: 84 loop : -2.05 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS D 330 PHE 0.012 0.001 PHE A 92 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7945 (m-90) cc_final: 0.7212 (t-100) REVERT: A 131 LEU cc_start: 0.9711 (mm) cc_final: 0.9365 (pp) REVERT: A 158 MET cc_start: 0.9212 (ppp) cc_final: 0.9004 (ppp) REVERT: A 191 GLU cc_start: 0.9306 (tt0) cc_final: 0.9081 (pp20) REVERT: A 400 MET cc_start: 0.9222 (mmm) cc_final: 0.8813 (tpp) REVERT: C 43 ASP cc_start: 0.9311 (p0) cc_final: 0.9044 (p0) REVERT: C 46 GLU cc_start: 0.9278 (tt0) cc_final: 0.8797 (pt0) REVERT: E 81 MET cc_start: 0.8987 (ttm) cc_final: 0.8682 (tpp) REVERT: E 121 TYR cc_start: 0.8786 (t80) cc_final: 0.8499 (t80) REVERT: E 141 ILE cc_start: 0.9618 (mm) cc_final: 0.9387 (tp) REVERT: F 66 MET cc_start: 0.9593 (mmm) cc_final: 0.9334 (mmm) REVERT: F 87 MET cc_start: 0.9481 (ttp) cc_final: 0.9064 (tmm) REVERT: F 101 GLN cc_start: 0.8733 (tt0) cc_final: 0.8382 (mt0) REVERT: F 107 PHE cc_start: 0.8621 (t80) cc_final: 0.8220 (t80) REVERT: F 128 ASP cc_start: 0.9128 (m-30) cc_final: 0.8846 (m-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2202 time to fit residues: 42.4950 Evaluate side-chains 81 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 347 GLN A 394 GLN A 398 GLN D 288 HIS D 307 GLN D 334 HIS D 416 ASN D 479 GLN D 494 GLN ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 10961 Z= 0.529 Angle : 0.806 14.236 14873 Z= 0.400 Chirality : 0.044 0.165 1777 Planarity : 0.005 0.045 1855 Dihedral : 3.911 20.637 1480 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.16 % Allowed : 14.21 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1322 helix: 1.14 (0.18), residues: 829 sheet: -2.32 (0.47), residues: 86 loop : -1.62 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 513 HIS 0.014 0.002 HIS D 334 PHE 0.027 0.002 PHE B 64 TYR 0.017 0.002 TYR A 139 ARG 0.004 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8448 (m-90) cc_final: 0.7341 (t-100) REVERT: A 158 MET cc_start: 0.9207 (ppp) cc_final: 0.8993 (ppp) REVERT: A 191 GLU cc_start: 0.9307 (tt0) cc_final: 0.9028 (pp20) REVERT: A 400 MET cc_start: 0.9047 (mmm) cc_final: 0.8736 (mmm) REVERT: C 46 GLU cc_start: 0.9234 (tt0) cc_final: 0.8601 (tp30) REVERT: B 59 PHE cc_start: 0.8678 (m-10) cc_final: 0.7461 (t80) REVERT: D 491 MET cc_start: 0.9103 (tmm) cc_final: 0.8525 (tpp) REVERT: D 608 MET cc_start: 0.9518 (mtm) cc_final: 0.9186 (mtm) REVERT: E 121 TYR cc_start: 0.8940 (t80) cc_final: 0.8491 (t80) REVERT: E 165 MET cc_start: 0.8692 (ttp) cc_final: 0.8321 (ppp) REVERT: E 200 ASN cc_start: 0.9537 (t0) cc_final: 0.9287 (t0) REVERT: F 66 MET cc_start: 0.9700 (mmm) cc_final: 0.9439 (mmm) REVERT: F 87 MET cc_start: 0.9522 (ttp) cc_final: 0.8979 (tmm) REVERT: F 101 GLN cc_start: 0.8668 (tt0) cc_final: 0.8359 (mt0) REVERT: F 114 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.8979 (p0) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1834 time to fit residues: 23.8480 Evaluate side-chains 72 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 114 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 134 optimal weight: 40.0000 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS D 558 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10961 Z= 0.204 Angle : 0.559 13.220 14873 Z= 0.270 Chirality : 0.039 0.202 1777 Planarity : 0.003 0.032 1855 Dihedral : 3.493 19.959 1480 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.61 % Allowed : 15.55 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1322 helix: 1.81 (0.18), residues: 835 sheet: -1.92 (0.48), residues: 90 loop : -1.30 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.003 0.001 HIS D 309 PHE 0.018 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8496 (m-90) cc_final: 0.7375 (t-100) REVERT: A 131 LEU cc_start: 0.9673 (mm) cc_final: 0.9425 (pp) REVERT: A 158 MET cc_start: 0.9186 (ppp) cc_final: 0.8975 (ppp) REVERT: A 191 GLU cc_start: 0.9242 (tt0) cc_final: 0.8916 (tm-30) REVERT: B 59 PHE cc_start: 0.8638 (m-10) cc_final: 0.7415 (t80) REVERT: D 608 MET cc_start: 0.9464 (mtm) cc_final: 0.9225 (mtm) REVERT: E 117 ILE cc_start: 0.9722 (mt) cc_final: 0.9449 (tt) REVERT: E 121 TYR cc_start: 0.8921 (t80) cc_final: 0.8444 (t80) REVERT: E 200 ASN cc_start: 0.9501 (t0) cc_final: 0.9263 (t0) REVERT: F 66 MET cc_start: 0.9667 (mmm) cc_final: 0.9387 (mmm) REVERT: F 71 GLN cc_start: 0.9252 (mt0) cc_final: 0.8986 (pt0) REVERT: F 87 MET cc_start: 0.9515 (ttp) cc_final: 0.9138 (tmm) REVERT: F 90 ARG cc_start: 0.9211 (mmm-85) cc_final: 0.8992 (mmm-85) REVERT: F 101 GLN cc_start: 0.8692 (tt0) cc_final: 0.8354 (mt0) REVERT: F 114 ASP cc_start: 0.9230 (m-30) cc_final: 0.9023 (p0) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.1777 time to fit residues: 25.1790 Evaluate side-chains 77 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 40.0000 chunk 83 optimal weight: 0.0570 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 40.0000 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10961 Z= 0.253 Angle : 0.582 12.934 14873 Z= 0.280 Chirality : 0.039 0.218 1777 Planarity : 0.003 0.032 1855 Dihedral : 3.479 20.306 1480 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 15.73 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1322 helix: 1.98 (0.18), residues: 839 sheet: -1.51 (0.50), residues: 88 loop : -1.09 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.004 0.001 HIS D 390 PHE 0.021 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.003 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 71 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8639 (m-90) cc_final: 0.7466 (t-100) REVERT: A 131 LEU cc_start: 0.9659 (mm) cc_final: 0.9406 (pp) REVERT: A 158 MET cc_start: 0.9225 (ppp) cc_final: 0.8998 (ppp) REVERT: A 191 GLU cc_start: 0.9234 (tt0) cc_final: 0.8921 (tm-30) REVERT: A 400 MET cc_start: 0.9150 (tpp) cc_final: 0.8709 (tpp) REVERT: B 59 PHE cc_start: 0.8642 (m-10) cc_final: 0.7419 (t80) REVERT: E 117 ILE cc_start: 0.9732 (mt) cc_final: 0.9447 (tt) REVERT: E 121 TYR cc_start: 0.8966 (t80) cc_final: 0.8487 (t80) REVERT: E 165 MET cc_start: 0.8752 (ttp) cc_final: 0.8236 (tmm) REVERT: E 200 ASN cc_start: 0.9542 (t0) cc_final: 0.9312 (t0) REVERT: F 66 MET cc_start: 0.9669 (mmm) cc_final: 0.9387 (mmm) REVERT: F 87 MET cc_start: 0.9557 (ttp) cc_final: 0.9211 (tmm) REVERT: F 90 ARG cc_start: 0.9275 (mmm-85) cc_final: 0.9018 (mmm-85) REVERT: F 101 GLN cc_start: 0.8757 (tt0) cc_final: 0.8404 (mt0) REVERT: F 128 ASP cc_start: 0.9319 (m-30) cc_final: 0.9046 (m-30) outliers start: 27 outliers final: 17 residues processed: 93 average time/residue: 0.1851 time to fit residues: 27.4124 Evaluate side-chains 82 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.2980 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10961 Z= 0.255 Angle : 0.578 12.070 14873 Z= 0.278 Chirality : 0.039 0.226 1777 Planarity : 0.003 0.031 1855 Dihedral : 3.480 17.541 1480 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.13 % Allowed : 15.91 % Favored : 80.97 % 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: 1.43 (0.24), residues: 1322 helix: 2.06 (0.18), residues: 843 sheet: -1.29 (0.52), residues: 88 loop : -1.02 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.003 0.001 HIS D 390 PHE 0.020 0.001 PHE B 66 TYR 0.013 0.001 TYR F 190 ARG 0.003 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 70 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8546 (m-90) cc_final: 0.7488 (t-100) REVERT: A 131 LEU cc_start: 0.9667 (mm) cc_final: 0.9414 (pp) REVERT: A 158 MET cc_start: 0.9241 (ppp) cc_final: 0.9013 (ppp) REVERT: A 191 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: A 450 LEU cc_start: 0.9532 (mp) cc_final: 0.9273 (mm) REVERT: B 59 PHE cc_start: 0.8648 (m-10) cc_final: 0.7362 (t80) REVERT: D 378 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8800 (p0) REVERT: E 117 ILE cc_start: 0.9748 (mt) cc_final: 0.9451 (tt) REVERT: E 121 TYR cc_start: 0.9009 (t80) cc_final: 0.8533 (t80) REVERT: E 165 MET cc_start: 0.8747 (ttp) cc_final: 0.8386 (ppp) REVERT: E 200 ASN cc_start: 0.9515 (t0) cc_final: 0.9280 (t0) REVERT: F 66 MET cc_start: 0.9659 (mmm) cc_final: 0.9407 (mmm) REVERT: F 87 MET cc_start: 0.9481 (ttp) cc_final: 0.8977 (tmm) REVERT: F 101 GLN cc_start: 0.8832 (tt0) cc_final: 0.8449 (mt0) REVERT: F 128 ASP cc_start: 0.9316 (m-30) cc_final: 0.9068 (m-30) outliers start: 35 outliers final: 22 residues processed: 99 average time/residue: 0.1918 time to fit residues: 29.3883 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10961 Z= 0.206 Angle : 0.557 11.382 14873 Z= 0.269 Chirality : 0.039 0.242 1777 Planarity : 0.003 0.031 1855 Dihedral : 3.417 20.237 1480 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.77 % Allowed : 16.98 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1322 helix: 2.15 (0.18), residues: 844 sheet: -1.12 (0.53), residues: 88 loop : -0.90 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.002 0.001 HIS D 309 PHE 0.025 0.001 PHE B 64 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8684 (m-90) cc_final: 0.7615 (t-100) REVERT: A 131 LEU cc_start: 0.9662 (mm) cc_final: 0.9406 (pp) REVERT: A 158 MET cc_start: 0.9243 (ppp) cc_final: 0.8996 (ppp) REVERT: A 191 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8889 (tm-30) REVERT: B 59 PHE cc_start: 0.8696 (m-10) cc_final: 0.7395 (t80) REVERT: E 117 ILE cc_start: 0.9752 (mt) cc_final: 0.9467 (tt) REVERT: E 121 TYR cc_start: 0.9049 (t80) cc_final: 0.8540 (t80) REVERT: E 165 MET cc_start: 0.8750 (ttp) cc_final: 0.8388 (ppp) REVERT: E 200 ASN cc_start: 0.9514 (t0) cc_final: 0.9258 (t0) REVERT: F 66 MET cc_start: 0.9644 (mmm) cc_final: 0.9353 (mmm) REVERT: F 90 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8967 (mtm110) REVERT: F 101 GLN cc_start: 0.8840 (tt0) cc_final: 0.8412 (mt0) outliers start: 31 outliers final: 20 residues processed: 92 average time/residue: 0.1794 time to fit residues: 26.4594 Evaluate side-chains 89 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 132 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10961 Z= 0.159 Angle : 0.556 13.066 14873 Z= 0.263 Chirality : 0.039 0.323 1777 Planarity : 0.003 0.032 1855 Dihedral : 3.303 20.641 1480 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 18.59 % Favored : 79.27 % 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: 1.78 (0.25), residues: 1322 helix: 2.28 (0.18), residues: 845 sheet: -1.04 (0.54), residues: 88 loop : -0.77 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS D 309 PHE 0.022 0.001 PHE B 66 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8683 (m-90) cc_final: 0.7692 (t60) REVERT: A 131 LEU cc_start: 0.9663 (mm) cc_final: 0.9426 (pp) REVERT: A 158 MET cc_start: 0.9220 (ppp) cc_final: 0.8971 (ppp) REVERT: A 191 GLU cc_start: 0.9237 (tt0) cc_final: 0.8926 (tm-30) REVERT: A 244 MET cc_start: 0.8678 (mtm) cc_final: 0.8084 (pmm) REVERT: A 400 MET cc_start: 0.9132 (tpp) cc_final: 0.8764 (tpp) REVERT: A 450 LEU cc_start: 0.9508 (mp) cc_final: 0.9282 (mm) REVERT: D 378 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (p0) REVERT: E 117 ILE cc_start: 0.9742 (mt) cc_final: 0.9454 (tt) REVERT: E 121 TYR cc_start: 0.9035 (t80) cc_final: 0.8608 (t80) REVERT: E 200 ASN cc_start: 0.9488 (t0) cc_final: 0.9249 (t0) REVERT: F 66 MET cc_start: 0.9612 (mmm) cc_final: 0.9357 (mmp) REVERT: F 90 ARG cc_start: 0.9380 (mmm-85) cc_final: 0.9095 (mtm110) REVERT: F 101 GLN cc_start: 0.8896 (tt0) cc_final: 0.8451 (mt0) REVERT: F 108 MET cc_start: 0.9446 (mtm) cc_final: 0.9176 (mtm) outliers start: 24 outliers final: 14 residues processed: 88 average time/residue: 0.1945 time to fit residues: 26.9649 Evaluate side-chains 82 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10961 Z= 0.199 Angle : 0.568 12.176 14873 Z= 0.272 Chirality : 0.039 0.259 1777 Planarity : 0.003 0.032 1855 Dihedral : 3.319 20.247 1480 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.97 % Allowed : 19.48 % Favored : 78.55 % 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: 1.82 (0.25), residues: 1322 helix: 2.29 (0.18), residues: 845 sheet: -1.01 (0.54), residues: 88 loop : -0.70 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.003 0.001 HIS D 334 PHE 0.022 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG E 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8704 (m-90) cc_final: 0.7678 (t-100) REVERT: A 131 LEU cc_start: 0.9658 (mm) cc_final: 0.9411 (pp) REVERT: A 158 MET cc_start: 0.9216 (ppp) cc_final: 0.8974 (ppp) REVERT: A 191 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8880 (tm-30) REVERT: A 244 MET cc_start: 0.8687 (mtm) cc_final: 0.8042 (pmm) REVERT: A 400 MET cc_start: 0.9111 (tpp) cc_final: 0.8740 (tpp) REVERT: A 450 LEU cc_start: 0.9515 (mp) cc_final: 0.9274 (mm) REVERT: B 59 PHE cc_start: 0.8703 (m-10) cc_final: 0.7456 (t80) REVERT: D 378 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (p0) REVERT: E 117 ILE cc_start: 0.9748 (mt) cc_final: 0.9458 (tt) REVERT: E 121 TYR cc_start: 0.9052 (t80) cc_final: 0.8587 (t80) REVERT: E 165 MET cc_start: 0.8856 (ttp) cc_final: 0.8578 (ppp) REVERT: E 200 ASN cc_start: 0.9473 (t0) cc_final: 0.9178 (t0) REVERT: F 66 MET cc_start: 0.9637 (mmm) cc_final: 0.9352 (mmm) REVERT: F 87 MET cc_start: 0.9552 (ttp) cc_final: 0.8836 (tmm) REVERT: F 90 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.9103 (mtm110) REVERT: F 101 GLN cc_start: 0.8890 (tt0) cc_final: 0.8460 (mt0) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.1821 time to fit residues: 24.7629 Evaluate side-chains 87 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10961 Z= 0.208 Angle : 0.575 11.622 14873 Z= 0.275 Chirality : 0.039 0.259 1777 Planarity : 0.003 0.031 1855 Dihedral : 3.351 19.745 1480 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.06 % Allowed : 19.39 % Favored : 78.55 % 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: 1.78 (0.25), residues: 1322 helix: 2.23 (0.18), residues: 847 sheet: -0.97 (0.54), residues: 88 loop : -0.66 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.008 0.001 HIS D 334 PHE 0.029 0.001 PHE B 64 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8692 (m-90) cc_final: 0.7677 (t60) REVERT: A 131 LEU cc_start: 0.9657 (mm) cc_final: 0.9413 (pp) REVERT: A 158 MET cc_start: 0.9201 (ppp) cc_final: 0.8955 (ppp) REVERT: A 191 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8872 (tm-30) REVERT: A 400 MET cc_start: 0.9115 (tpp) cc_final: 0.8739 (tpp) REVERT: B 59 PHE cc_start: 0.8728 (m-10) cc_final: 0.7466 (t80) REVERT: D 378 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (p0) REVERT: E 117 ILE cc_start: 0.9750 (mt) cc_final: 0.9474 (tt) REVERT: E 121 TYR cc_start: 0.9024 (t80) cc_final: 0.8553 (t80) REVERT: E 165 MET cc_start: 0.8831 (ttp) cc_final: 0.8533 (ppp) REVERT: E 200 ASN cc_start: 0.9500 (t0) cc_final: 0.9229 (t0) REVERT: F 66 MET cc_start: 0.9637 (mmm) cc_final: 0.9373 (mmm) REVERT: F 90 ARG cc_start: 0.9381 (mmm-85) cc_final: 0.9116 (mtm110) REVERT: F 101 GLN cc_start: 0.8921 (tt0) cc_final: 0.8485 (mt0) REVERT: F 128 ASP cc_start: 0.9299 (m-30) cc_final: 0.9051 (m-30) outliers start: 23 outliers final: 18 residues processed: 83 average time/residue: 0.1812 time to fit residues: 24.1681 Evaluate side-chains 87 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 136 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10961 Z= 0.186 Angle : 0.591 15.346 14873 Z= 0.280 Chirality : 0.039 0.266 1777 Planarity : 0.003 0.031 1855 Dihedral : 3.316 19.604 1480 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.88 % Allowed : 19.39 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1322 helix: 2.20 (0.18), residues: 849 sheet: -0.89 (0.55), residues: 88 loop : -0.59 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.006 0.001 HIS D 334 PHE 0.026 0.001 PHE B 64 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8720 (m-90) cc_final: 0.7700 (t60) REVERT: A 131 LEU cc_start: 0.9653 (mm) cc_final: 0.9411 (pp) REVERT: A 158 MET cc_start: 0.9213 (ppp) cc_final: 0.8988 (ppp) REVERT: A 191 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8901 (tm-30) REVERT: A 244 MET cc_start: 0.8703 (mtm) cc_final: 0.8117 (mmp) REVERT: A 400 MET cc_start: 0.9112 (tpp) cc_final: 0.8728 (tpp) REVERT: B 59 PHE cc_start: 0.8711 (m-10) cc_final: 0.7473 (t80) REVERT: D 378 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8661 (p0) REVERT: E 117 ILE cc_start: 0.9745 (mt) cc_final: 0.9474 (tt) REVERT: E 121 TYR cc_start: 0.9020 (t80) cc_final: 0.8559 (t80) REVERT: E 165 MET cc_start: 0.8854 (ttp) cc_final: 0.8574 (ppp) REVERT: E 200 ASN cc_start: 0.9494 (t0) cc_final: 0.9220 (t0) REVERT: F 66 MET cc_start: 0.9621 (mmm) cc_final: 0.9353 (mmm) REVERT: F 87 MET cc_start: 0.9567 (ttp) cc_final: 0.8844 (tmm) REVERT: F 90 ARG cc_start: 0.9384 (mmm-85) cc_final: 0.9133 (mtm110) REVERT: F 101 GLN cc_start: 0.8876 (tt0) cc_final: 0.8443 (mt0) REVERT: F 128 ASP cc_start: 0.9263 (m-30) cc_final: 0.9026 (m-30) outliers start: 21 outliers final: 18 residues processed: 83 average time/residue: 0.1798 time to fit residues: 23.9073 Evaluate side-chains 87 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** 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 = 0.3087 r_free = 0.3087 target = 0.046941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.035669 restraints weight = 76560.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036664 restraints weight = 42474.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.037303 restraints weight = 28617.769| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10961 Z= 0.186 Angle : 0.601 18.207 14873 Z= 0.282 Chirality : 0.039 0.264 1777 Planarity : 0.003 0.031 1855 Dihedral : 3.283 19.341 1480 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 19.48 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1322 helix: 2.22 (0.18), residues: 851 sheet: -0.82 (0.55), residues: 88 loop : -0.50 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.006 0.001 HIS D 334 PHE 0.027 0.001 PHE B 64 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.15 seconds wall clock time: 33 minutes 7.35 seconds (1987.35 seconds total)