Starting phenix.real_space_refine on Fri Mar 15 05:33:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kap_22779/03_2024/7kap_22779.pdb" } resolution = 4.1 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= 0.009 sd= 0.063 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 38 5.16 5 C 6980 2.51 5 N 1807 2.21 5 O 1890 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 196": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" 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 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-5265/modules/chem_data/mon_lib" Total number of atoms: 10715 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3307 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 415} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 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: 5.76, per 1000 atoms: 0.54 Number of scatterers: 10715 At special positions: 0 Unit cell: (109.25, 124.2, 136.85, 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 38 16.00 O 1890 8.00 N 1807 7.00 C 6980 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: 4.39 Conformation dependent library (CDL) restraints added in 2.0 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 70.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.789A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.893A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 199 removed outlier: 3.609A pdb=" N ALA A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.571A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.162A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 290 through 314 removed outlier: 4.094A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.528A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.501A pdb=" N TYR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.593A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.810A 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 63 removed outlier: 4.323A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.580A pdb=" N PHE D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) 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: 3.583A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.880A 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 removed outlier: 3.728A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.524A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.895A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.537A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.847A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.127A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.766A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 422 removed outlier: 4.205A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 490 through 494 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.591A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.534A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 3.721A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.990A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 3.817A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.337A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.846A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.865A 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 removed outlier: 3.638A pdb=" N SER F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.704A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.454A 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: 3.877A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.531A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK G 166 " --> pdb=" O UNK G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 removed outlier: 3.525A pdb=" N UNK G 205 " --> pdb=" O UNK G 201 " (cutoff:3.500A) 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 326 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 3.600A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.669A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 692 hydrogen bonds defined for protein. 2028 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: 2.95 Time building geometry restraints manager: 4.73 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: 3396 1.34 - 1.46: 2366 1.46 - 1.58: 5100 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 10921 Sorted by residual: bond pdb=" C ILE D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.334 1.324 0.010 1.11e-02 8.12e+03 7.55e-01 bond pdb=" CB PRO A 84 " pdb=" CG PRO A 84 " ideal model delta sigma weight residual 1.492 1.454 0.038 5.00e-02 4.00e+02 5.76e-01 bond pdb=" CA LEU F 102 " pdb=" C LEU F 102 " ideal model delta sigma weight residual 1.521 1.529 -0.009 1.14e-02 7.69e+03 5.69e-01 bond pdb=" C LYS D 493 " pdb=" N GLN D 494 " ideal model delta sigma weight residual 1.340 1.298 0.042 5.87e-02 2.90e+02 5.19e-01 bond pdb=" C TRP D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.15e-01 ... (remaining 10916 not shown) Histogram of bond angle deviations from ideal: 100.24 - 106.99: 302 106.99 - 113.74: 6342 113.74 - 120.49: 4282 120.49 - 127.23: 3787 127.23 - 133.98: 105 Bond angle restraints: 14818 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 120.33 122.23 -1.90 8.00e-01 1.56e+00 5.65e+00 angle pdb=" N VAL E 160 " pdb=" CA VAL E 160 " pdb=" C VAL E 160 " ideal model delta sigma weight residual 111.90 110.01 1.89 8.10e-01 1.52e+00 5.43e+00 angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 114.00 111.00 3.00 1.31e+00 5.83e-01 5.25e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.55 114.11 -3.56 1.63e+00 3.76e-01 4.76e+00 angle pdb=" CA LEU A 162 " pdb=" CB LEU A 162 " pdb=" CG LEU A 162 " ideal model delta sigma weight residual 116.30 123.64 -7.34 3.50e+00 8.16e-02 4.40e+00 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6248 17.95 - 35.90: 262 35.90 - 53.86: 46 53.86 - 71.81: 10 71.81 - 89.76: 8 Dihedral angle restraints: 6574 sinusoidal: 2509 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ASP E 201 " pdb=" CB ASP E 201 " pdb=" CG ASP E 201 " pdb=" OD1 ASP E 201 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU C 31 " pdb=" CG GLU C 31 " pdb=" CD GLU C 31 " pdb=" OE1 GLU C 31 " ideal model delta sinusoidal sigma weight residual 0.00 -89.76 89.76 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 472 " pdb=" CG GLU D 472 " pdb=" CD GLU D 472 " pdb=" OE1 GLU D 472 " ideal model delta sinusoidal sigma weight residual 0.00 -87.61 87.61 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1048 0.026 - 0.053: 467 0.053 - 0.079: 162 0.079 - 0.105: 79 0.105 - 0.132: 15 Chirality restraints: 1771 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 4.34e-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 3.76e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1768 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 463 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO F 48 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO F 94 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.018 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1268 2.74 - 3.28: 11240 3.28 - 3.82: 17674 3.82 - 4.36: 19269 4.36 - 4.90: 34039 Nonbonded interactions: 83490 Sorted by model distance: nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.205 2.520 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.248 2.440 nonbonded pdb=" NZ LYS A 284 " pdb=" OE1 GLU A 460 " model vdw 2.276 2.520 nonbonded pdb=" OE2 GLU E 151 " pdb=" NH2 ARG E 154 " model vdw 2.309 2.520 nonbonded pdb=" NH2 ARG D 458 " pdb=" O GLN D 462 " model vdw 2.317 2.520 ... (remaining 83485 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 4.020 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 30.480 Find NCS groups from input model: 0.300 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.042 10921 Z= 0.176 Angle : 0.545 11.785 14818 Z= 0.287 Chirality : 0.037 0.132 1771 Planarity : 0.003 0.039 1850 Dihedral : 11.241 89.758 3932 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -1.05 (0.22), residues: 1318 helix: 0.26 (0.17), residues: 818 sheet: -2.91 (0.44), residues: 86 loop : -2.02 (0.29), residues: 414 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 0.009 0.001 PHE A 92 TYR 0.014 0.001 TYR F 190 ARG 0.002 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8786 (t80) cc_final: 0.8393 (t80) REVERT: A 169 GLU cc_start: 0.9369 (tp30) cc_final: 0.8959 (tp30) REVERT: A 249 MET cc_start: 0.8686 (mmp) cc_final: 0.8401 (mmm) REVERT: A 349 LEU cc_start: 0.8521 (mt) cc_final: 0.8277 (tt) REVERT: A 376 PHE cc_start: 0.9438 (m-10) cc_final: 0.9163 (m-10) REVERT: A 380 TRP cc_start: 0.8992 (t-100) cc_final: 0.8512 (t-100) REVERT: C 43 ASP cc_start: 0.8556 (p0) cc_final: 0.7757 (p0) REVERT: D 100 TRP cc_start: 0.9603 (m100) cc_final: 0.9029 (m100) REVERT: E 81 MET cc_start: 0.9359 (ttm) cc_final: 0.9101 (mtp) REVERT: E 141 ILE cc_start: 0.9350 (mm) cc_final: 0.8957 (tt) REVERT: F 57 MET cc_start: 0.9215 (mtp) cc_final: 0.9006 (ptp) REVERT: F 66 MET cc_start: 0.9188 (mmp) cc_final: 0.8980 (mmm) REVERT: F 101 GLN cc_start: 0.9366 (tt0) cc_final: 0.8768 (pt0) REVERT: F 108 MET cc_start: 0.9241 (mtm) cc_final: 0.8756 (mtm) REVERT: F 118 ILE cc_start: 0.9760 (mt) cc_final: 0.9515 (tp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2364 time to fit residues: 51.7369 Evaluate side-chains 80 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 156 GLN A 188 ASN A 192 GLN A 394 GLN A 398 GLN A 403 ASN D 4 ASN D 33 GLN D 113 ASN D 307 GLN D 416 ASN D 474 ASN D 494 GLN E 88 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN F 68 ASN F 106 HIS F 155 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10921 Z= 0.195 Angle : 0.546 13.726 14818 Z= 0.263 Chirality : 0.038 0.204 1771 Planarity : 0.003 0.036 1850 Dihedral : 3.187 13.753 1476 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % 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: 0.36 (0.24), residues: 1318 helix: 1.39 (0.18), residues: 836 sheet: -2.25 (0.43), residues: 100 loop : -1.61 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.003 0.001 HIS D 330 PHE 0.008 0.001 PHE A 256 TYR 0.014 0.001 TYR F 190 ARG 0.006 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.9379 (tp30) cc_final: 0.9009 (tp30) REVERT: A 249 MET cc_start: 0.8865 (mmp) cc_final: 0.8626 (tpp) REVERT: A 349 LEU cc_start: 0.8732 (mt) cc_final: 0.8396 (tt) REVERT: A 380 TRP cc_start: 0.9004 (t-100) cc_final: 0.8560 (t-100) REVERT: C 31 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8690 (mm-30) REVERT: D 100 TRP cc_start: 0.9609 (m100) cc_final: 0.9042 (m100) REVERT: D 608 MET cc_start: 0.8767 (ptp) cc_final: 0.8566 (ptp) REVERT: E 150 GLN cc_start: 0.9794 (tm-30) cc_final: 0.9577 (pp30) REVERT: E 174 GLN cc_start: 0.9361 (tt0) cc_final: 0.9120 (tp40) REVERT: F 66 MET cc_start: 0.9163 (mmp) cc_final: 0.8927 (mmm) REVERT: F 90 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8374 (tpp80) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2043 time to fit residues: 31.5900 Evaluate side-chains 69 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 192 GLN D 330 HIS D 381 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10921 Z= 0.183 Angle : 0.527 12.700 14818 Z= 0.251 Chirality : 0.037 0.133 1771 Planarity : 0.003 0.035 1850 Dihedral : 3.227 15.230 1476 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 1.04 (0.24), residues: 1318 helix: 1.88 (0.18), residues: 832 sheet: -1.89 (0.44), residues: 98 loop : -1.23 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 95 HIS 0.003 0.001 HIS D 330 PHE 0.007 0.001 PHE D 343 TYR 0.014 0.001 TYR E 75 ARG 0.002 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.9366 (tp30) cc_final: 0.8999 (tp30) REVERT: A 249 MET cc_start: 0.8870 (mmp) cc_final: 0.8608 (tpp) REVERT: A 380 TRP cc_start: 0.8987 (t-100) cc_final: 0.8572 (t-100) REVERT: C 31 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8670 (mm-30) REVERT: C 40 LYS cc_start: 0.9263 (tmtt) cc_final: 0.8919 (tptt) REVERT: C 49 LYS cc_start: 0.9426 (ptmt) cc_final: 0.9184 (ptmm) REVERT: B 76 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9190 (tptt) REVERT: D 100 TRP cc_start: 0.9611 (m100) cc_final: 0.9017 (m100) REVERT: D 608 MET cc_start: 0.8965 (ptp) cc_final: 0.8661 (ptp) REVERT: E 141 ILE cc_start: 0.9421 (mm) cc_final: 0.9034 (tt) REVERT: E 150 GLN cc_start: 0.9796 (tm-30) cc_final: 0.9588 (pp30) REVERT: E 174 GLN cc_start: 0.9388 (tt0) cc_final: 0.9155 (tp40) REVERT: F 90 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8381 (tpp80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2073 time to fit residues: 30.4731 Evaluate side-chains 69 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10921 Z= 0.300 Angle : 0.597 13.664 14818 Z= 0.293 Chirality : 0.039 0.162 1771 Planarity : 0.004 0.037 1850 Dihedral : 3.511 17.006 1476 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 1.31 (0.24), residues: 1318 helix: 1.99 (0.18), residues: 834 sheet: -1.48 (0.46), residues: 97 loop : -0.96 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 159 HIS 0.005 0.001 HIS E 88 PHE 0.009 0.001 PHE D 74 TYR 0.014 0.001 TYR F 190 ARG 0.004 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.9321 (tp30) cc_final: 0.8934 (tp30) REVERT: A 249 MET cc_start: 0.8883 (mmp) cc_final: 0.8623 (tpp) REVERT: A 380 TRP cc_start: 0.9017 (t-100) cc_final: 0.8675 (t-100) REVERT: C 31 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8671 (mm-30) REVERT: C 40 LYS cc_start: 0.9240 (tmtt) cc_final: 0.8904 (tptt) REVERT: B 76 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9196 (tptt) REVERT: D 100 TRP cc_start: 0.9641 (m100) cc_final: 0.9024 (m100) REVERT: D 608 MET cc_start: 0.9191 (ptp) cc_final: 0.8825 (ptp) REVERT: E 141 ILE cc_start: 0.9451 (mm) cc_final: 0.9088 (tt) REVERT: F 66 MET cc_start: 0.9188 (mmp) cc_final: 0.8957 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2119 time to fit residues: 28.3593 Evaluate side-chains 63 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 113 optimal weight: 0.0050 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN E 84 ASN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10921 Z= 0.129 Angle : 0.518 11.795 14818 Z= 0.243 Chirality : 0.038 0.157 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.328 17.136 1476 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 1.59 (0.24), residues: 1318 helix: 2.16 (0.18), residues: 832 sheet: -1.40 (0.48), residues: 88 loop : -0.75 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.004 0.001 HIS D 330 PHE 0.020 0.001 PHE A 254 TYR 0.013 0.001 TYR E 75 ARG 0.002 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.9321 (tp30) cc_final: 0.8935 (tp30) REVERT: A 249 MET cc_start: 0.8869 (mmp) cc_final: 0.8576 (tpp) REVERT: A 380 TRP cc_start: 0.8968 (t-100) cc_final: 0.8581 (t-100) REVERT: C 31 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8599 (mm-30) REVERT: C 40 LYS cc_start: 0.9242 (tmtt) cc_final: 0.8853 (tptt) REVERT: B 76 LYS cc_start: 0.9414 (tmtt) cc_final: 0.9195 (tptt) REVERT: D 100 TRP cc_start: 0.9636 (m100) cc_final: 0.9290 (m100) REVERT: D 608 MET cc_start: 0.9102 (ptp) cc_final: 0.8876 (ptp) REVERT: E 141 ILE cc_start: 0.9415 (mm) cc_final: 0.9048 (tt) REVERT: E 150 GLN cc_start: 0.9798 (tm-30) cc_final: 0.9596 (pp30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2001 time to fit residues: 30.2322 Evaluate side-chains 69 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10921 Z= 0.169 Angle : 0.525 12.165 14818 Z= 0.250 Chirality : 0.038 0.133 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.328 17.016 1476 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.79 (0.24), residues: 1318 helix: 2.27 (0.18), residues: 833 sheet: -1.16 (0.47), residues: 97 loop : -0.58 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 14 HIS 0.003 0.001 HIS E 88 PHE 0.014 0.001 PHE A 254 TYR 0.012 0.001 TYR E 75 ARG 0.002 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9022 (t80) cc_final: 0.8688 (t80) REVERT: A 169 GLU cc_start: 0.9314 (tp30) cc_final: 0.8927 (tp30) REVERT: A 249 MET cc_start: 0.8894 (mmp) cc_final: 0.8620 (tpp) REVERT: A 380 TRP cc_start: 0.8965 (t-100) cc_final: 0.8575 (t-100) REVERT: C 31 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8615 (mm-30) REVERT: C 40 LYS cc_start: 0.9398 (tmtt) cc_final: 0.9032 (tptt) REVERT: B 76 LYS cc_start: 0.9420 (tmtt) cc_final: 0.9201 (tptt) REVERT: D 100 TRP cc_start: 0.9625 (m100) cc_final: 0.9018 (m100) REVERT: D 347 ASP cc_start: 0.8911 (t70) cc_final: 0.8613 (t0) REVERT: D 608 MET cc_start: 0.9163 (ptp) cc_final: 0.8819 (ptp) REVERT: E 141 ILE cc_start: 0.9430 (mm) cc_final: 0.9089 (tt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1823 time to fit residues: 26.5693 Evaluate side-chains 67 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 82 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 0.0060 chunk 81 optimal weight: 7.9990 overall best weight: 2.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10921 Z= 0.186 Angle : 0.533 12.160 14818 Z= 0.253 Chirality : 0.038 0.167 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.350 17.245 1476 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.91 (0.24), residues: 1318 helix: 2.33 (0.18), residues: 834 sheet: -1.15 (0.49), residues: 87 loop : -0.48 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 14 HIS 0.002 0.001 HIS C 72 PHE 0.013 0.001 PHE A 254 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8973 (t80) cc_final: 0.8704 (t80) REVERT: A 169 GLU cc_start: 0.9317 (tp30) cc_final: 0.8929 (tp30) REVERT: A 249 MET cc_start: 0.8879 (mmp) cc_final: 0.8588 (tpp) REVERT: A 285 LEU cc_start: 0.9457 (tp) cc_final: 0.9249 (tp) REVERT: A 380 TRP cc_start: 0.8922 (t-100) cc_final: 0.8542 (t-100) REVERT: A 400 MET cc_start: 0.9480 (mmp) cc_final: 0.9261 (mmm) REVERT: C 31 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8623 (mm-30) REVERT: C 40 LYS cc_start: 0.9418 (tmtt) cc_final: 0.9048 (tptt) REVERT: B 59 PHE cc_start: 0.9067 (m-10) cc_final: 0.8599 (t80) REVERT: B 76 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9204 (tptt) REVERT: D 100 TRP cc_start: 0.9655 (m100) cc_final: 0.9040 (m100) REVERT: D 347 ASP cc_start: 0.8872 (t70) cc_final: 0.8578 (t0) REVERT: D 608 MET cc_start: 0.9146 (ptp) cc_final: 0.8789 (ptp) REVERT: F 87 MET cc_start: 0.9111 (tpt) cc_final: 0.8794 (tpp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1983 time to fit residues: 26.8363 Evaluate side-chains 64 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10921 Z= 0.248 Angle : 0.569 12.769 14818 Z= 0.276 Chirality : 0.039 0.131 1771 Planarity : 0.003 0.037 1850 Dihedral : 3.506 17.331 1476 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.94 (0.24), residues: 1318 helix: 2.32 (0.18), residues: 835 sheet: -1.02 (0.48), residues: 97 loop : -0.39 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 159 HIS 0.004 0.001 HIS E 88 PHE 0.015 0.001 PHE D 343 TYR 0.013 0.001 TYR F 190 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8979 (t80) cc_final: 0.8637 (t80) REVERT: A 169 GLU cc_start: 0.9277 (tp30) cc_final: 0.8903 (tp30) REVERT: A 249 MET cc_start: 0.8924 (mmp) cc_final: 0.8615 (tpp) REVERT: A 261 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8916 (mm-40) REVERT: A 380 TRP cc_start: 0.8943 (t-100) cc_final: 0.8567 (t-100) REVERT: A 400 MET cc_start: 0.9499 (mmp) cc_final: 0.9289 (mmm) REVERT: C 31 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8664 (mm-30) REVERT: C 40 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9064 (tptt) REVERT: B 59 PHE cc_start: 0.9101 (m-10) cc_final: 0.8610 (t80) REVERT: D 347 ASP cc_start: 0.8890 (t70) cc_final: 0.8574 (t0) REVERT: D 608 MET cc_start: 0.9202 (ptp) cc_final: 0.8888 (ptp) REVERT: E 141 ILE cc_start: 0.9450 (mm) cc_final: 0.9121 (tt) REVERT: F 108 MET cc_start: 0.9354 (mtm) cc_final: 0.8740 (mtm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1871 time to fit residues: 25.5427 Evaluate side-chains 63 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10921 Z= 0.196 Angle : 0.548 12.392 14818 Z= 0.261 Chirality : 0.038 0.133 1771 Planarity : 0.003 0.039 1850 Dihedral : 3.487 16.775 1476 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 2.00 (0.24), residues: 1318 helix: 2.35 (0.18), residues: 835 sheet: -0.97 (0.51), residues: 87 loop : -0.34 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 14 HIS 0.003 0.001 HIS C 72 PHE 0.012 0.001 PHE A 254 TYR 0.011 0.001 TYR F 190 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.9280 (tp30) cc_final: 0.8885 (tp30) REVERT: A 249 MET cc_start: 0.8923 (mmp) cc_final: 0.8647 (tpp) REVERT: A 380 TRP cc_start: 0.8911 (t-100) cc_final: 0.8546 (t-100) REVERT: C 31 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8595 (mm-30) REVERT: C 40 LYS cc_start: 0.9401 (tmtt) cc_final: 0.9073 (tptt) REVERT: B 59 PHE cc_start: 0.9103 (m-10) cc_final: 0.8591 (t80) REVERT: D 347 ASP cc_start: 0.8844 (t70) cc_final: 0.8526 (t0) REVERT: D 608 MET cc_start: 0.9167 (ptp) cc_final: 0.8825 (ptp) REVERT: E 141 ILE cc_start: 0.9449 (mm) cc_final: 0.9122 (tt) REVERT: F 108 MET cc_start: 0.9346 (mtm) cc_final: 0.8722 (mtm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1928 time to fit residues: 26.3611 Evaluate side-chains 60 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 136 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10921 Z= 0.127 Angle : 0.521 11.655 14818 Z= 0.243 Chirality : 0.037 0.137 1771 Planarity : 0.003 0.040 1850 Dihedral : 3.349 16.285 1476 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 2.13 (0.24), residues: 1318 helix: 2.43 (0.18), residues: 836 sheet: -0.81 (0.52), residues: 87 loop : -0.27 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 14 HIS 0.002 0.001 HIS F 122 PHE 0.015 0.001 PHE A 254 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG F 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8761 (mmt) cc_final: 0.8557 (ppp) REVERT: A 169 GLU cc_start: 0.9208 (tp30) cc_final: 0.8909 (tp30) REVERT: A 249 MET cc_start: 0.8867 (mmp) cc_final: 0.8593 (tpp) REVERT: A 380 TRP cc_start: 0.8871 (t-100) cc_final: 0.8510 (t-100) REVERT: C 31 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 40 LYS cc_start: 0.9415 (tmtt) cc_final: 0.9035 (tptt) REVERT: B 59 PHE cc_start: 0.9086 (m-10) cc_final: 0.8522 (t80) REVERT: D 347 ASP cc_start: 0.8802 (t70) cc_final: 0.8497 (t0) REVERT: D 608 MET cc_start: 0.9104 (ptp) cc_final: 0.8838 (ptp) REVERT: E 141 ILE cc_start: 0.9449 (mm) cc_final: 0.9118 (tt) REVERT: F 108 MET cc_start: 0.9322 (mtm) cc_final: 0.8703 (mtm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1937 time to fit residues: 26.7179 Evaluate side-chains 62 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 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 = 0.3147 r_free = 0.3147 target = 0.047344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.037235 restraints weight = 79614.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038223 restraints weight = 44200.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038927 restraints weight = 29728.035| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10921 Z= 0.170 Angle : 0.538 12.023 14818 Z= 0.252 Chirality : 0.037 0.135 1771 Planarity : 0.003 0.039 1850 Dihedral : 3.351 16.330 1476 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 2.14 (0.24), residues: 1318 helix: 2.39 (0.18), residues: 844 sheet: -0.85 (0.51), residues: 87 loop : -0.20 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 14 HIS 0.002 0.001 HIS C 72 PHE 0.012 0.001 PHE A 159 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG E 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.29 seconds wall clock time: 33 minutes 8.37 seconds (1988.37 seconds total)