Starting phenix.real_space_refine on Fri Mar 15 11:15:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/03_2024/4uis_2974_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2965 atoms to isotropic. 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 32 5.16 5 C 5352 2.51 5 N 1523 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4372 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 555} Chain breaks: 12 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1522 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 2, 'TRANS': 238} Chain breaks: 6 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 969 Classifications: {'peptide': 196} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 185} Link IDs: {'CIS': 1, 'TRANS': 194} Chain breaks: 4 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 196} Unresolved non-hydrogen planarities: 196 Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 306 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 58} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 1349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 bond proxies already assigned to first conformer: 1250 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AGLU G 5 " occ=0.32 ... (16 atoms not shown) pdb=" OE2BGLU G 5 " occ=0.68 residue: pdb=" N AARG G 76 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG G 76 " occ=0.43 residue: pdb=" N ALYS G 135 " occ=0.29 ... (16 atoms not shown) pdb=" NZ BLYS G 135 " occ=0.71 residue: pdb=" N AARG G 137 " occ=0.41 ... (20 atoms not shown) pdb=" NH2BARG G 137 " occ=0.59 residue: pdb=" N AASN G 140 " occ=0.46 ... (14 atoms not shown) pdb=" ND2BASN G 140 " occ=0.54 residue: pdb=" N AGLN G 141 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN G 141 " occ=0.54 Time building chain proxies: 5.40, per 1000 atoms: 0.63 Number of scatterers: 8518 At special positions: 0 Unit cell: (122.76, 113.52, 142.56, 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 32 16.00 O 1611 8.00 N 1523 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.04 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 97.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.440A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.042A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 removed outlier: 4.087A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 199 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.707A pdb=" N PHE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.652A pdb=" N VAL A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.753A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.089A pdb=" N SER A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.774A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.988A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.583A pdb=" N ASP A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 542 " --> pdb=" O ARG A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.584A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 665 through 687 removed outlier: 3.576A pdb=" N UNK A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 101 removed outlier: 3.723A pdb=" N UNK B 73 " --> pdb=" O UNK B 69 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.679A pdb=" N UNK B 171 " --> pdb=" O UNK B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.570A pdb=" N UNK B 198 " --> pdb=" O UNK B 194 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK B 216 " --> pdb=" O UNK B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.671A pdb=" N GLN B 222 " --> pdb=" O UNK B 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK B 241 " --> pdb=" O UNK B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.851A pdb=" N UNK B 250 " --> pdb=" O UNK B 246 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 257 " --> pdb=" O UNK B 253 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK B 265 " --> pdb=" O UNK B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.941A pdb=" N UNK B 399 " --> pdb=" O UNK B 395 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK B 400 " --> pdb=" O UNK B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.505A pdb=" N UNK B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.672A pdb=" N UNK B 438 " --> pdb=" O UNK B 434 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 444 " --> pdb=" O UNK B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.645A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.389A pdb=" N UNK C 18 " --> pdb=" O UNK C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 56 removed outlier: 4.133A pdb=" N UNK C 40 " --> pdb=" O UNK C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 102 removed outlier: 3.851A pdb=" N UNK C 86 " --> pdb=" O UNK C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK C 87 " --> pdb=" O UNK C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 152 through 178 removed outlier: 4.032A pdb=" N UNK C 156 " --> pdb=" O UNK C 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK C 177 " --> pdb=" O UNK C 173 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK C 178 " --> pdb=" O UNK C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.744A pdb=" N UNK C 183 " --> pdb=" O UNK C 179 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK C 184 " --> pdb=" O UNK C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.643A pdb=" N UNK C 188 " --> pdb=" O UNK C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 220 removed outlier: 4.123A pdb=" N UNK C 208 " --> pdb=" O UNK C 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK C 213 " --> pdb=" O UNK C 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK C 214 " --> pdb=" O UNK C 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK C 215 " --> pdb=" O UNK C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.057A pdb=" N UNK D 13 " --> pdb=" O UNK D 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK D 16 " --> pdb=" O UNK D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.753A pdb=" N UNK D 25 " --> pdb=" O UNK D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 72 removed outlier: 4.028A pdb=" N UNK D 47 " --> pdb=" O UNK D 43 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK D 49 " --> pdb=" O UNK D 45 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNK D 50 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK D 51 " --> pdb=" O UNK D 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N UNK D 55 " --> pdb=" O UNK D 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK D 65 " --> pdb=" O UNK D 61 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N UNK D 66 " --> pdb=" O UNK D 62 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N UNK D 67 " --> pdb=" O UNK D 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 38 through 51 removed outlier: 3.888A pdb=" N ALA G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 83 through 91 removed outlier: 3.924A pdb=" N VAL G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.969A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 142 through 156 Processing helix chain 'G' and resid 158 through 162 Processing sheet with id= AA, first strand: chain 'A' and resid 47 through 48 Processing sheet with id= AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id= AC, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.378A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= AE, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.813A pdb=" N ASP A 253 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.735A pdb=" N VAL A 276 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 280 through 281 Processing sheet with id= AH, first strand: chain 'A' and resid 365 through 366 Processing sheet with id= AI, first strand: chain 'A' and resid 605 through 606 Processing sheet with id= GA, first strand: chain 'G' and resid 17 through 19 removed outlier: 7.694A pdb=" N TYR G 25 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1554 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: 2.30 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2893 1.34 - 1.46: 1592 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 8625 Sorted by residual: bond pdb=" CA PHE A 302 " pdb=" C PHE A 302 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.27e-02 6.20e+03 1.10e+01 bond pdb=" CA VAL A 256 " pdb=" CB VAL A 256 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.36e-02 5.41e+03 7.32e+00 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.25e-02 6.40e+03 6.39e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.51e-02 4.39e+03 5.94e+00 bond pdb=" C ALA A 556 " pdb=" O ALA A 556 " ideal model delta sigma weight residual 1.239 1.215 0.023 9.60e-03 1.09e+04 5.94e+00 ... (remaining 8620 not shown) Histogram of bond angle deviations from ideal: 99.49 - 107.11: 232 107.11 - 114.74: 5095 114.74 - 122.37: 4811 122.37 - 129.99: 1571 129.99 - 137.62: 55 Bond angle restraints: 11764 Sorted by residual: angle pdb=" C GLY A 89 " pdb=" N PRO A 90 " pdb=" CA PRO A 90 " ideal model delta sigma weight residual 119.84 109.60 10.24 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N VAL A 85 " pdb=" CA VAL A 85 " pdb=" C VAL A 85 " ideal model delta sigma weight residual 111.67 104.39 7.28 9.50e-01 1.11e+00 5.87e+01 angle pdb=" N LEU A 542 " pdb=" CA LEU A 542 " pdb=" C LEU A 542 " ideal model delta sigma weight residual 108.23 117.36 -9.13 1.38e+00 5.25e-01 4.38e+01 angle pdb=" C ALA A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.78 126.51 -6.73 1.03e+00 9.43e-01 4.26e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 ... (remaining 11759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4968 17.72 - 35.44: 120 35.44 - 53.16: 26 53.16 - 70.88: 3 70.88 - 88.60: 5 Dihedral angle restraints: 5122 sinusoidal: 1481 harmonic: 3641 Sorted by residual: dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLN A 552 " pdb=" C GLN A 552 " pdb=" N HIS A 553 " pdb=" CA HIS A 553 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N GLN A 454 " pdb=" CA GLN A 454 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 5119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.118: 365 0.118 - 0.177: 41 0.177 - 0.236: 7 0.236 - 0.295: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CB ILE A 338 " pdb=" CA ILE A 338 " pdb=" CG1 ILE A 338 " pdb=" CG2 ILE A 338 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA CYS A 159 " pdb=" N CYS A 159 " pdb=" C CYS A 159 " pdb=" CB CYS A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA UNK A 626 " pdb=" N UNK A 626 " pdb=" C UNK A 626 " pdb=" CB UNK A 626 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1435 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 164 " 0.018 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 164 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 164 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 473 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 138 " -0.018 2.00e-02 2.50e+03 1.33e-02 4.39e+00 pdb=" CG TRP G 138 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP G 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 138 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 138 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 138 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 138 " -0.001 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 3660 2.89 - 3.56: 13504 3.56 - 4.23: 18838 4.23 - 4.90: 29789 Nonbonded interactions: 65808 Sorted by model distance: nonbonded pdb=" O UNK D 42 " pdb=" N UNK D 44 " model vdw 1.546 2.520 nonbonded pdb=" OE2 GLU G 11 " pdb=" NH1 ARG G 145 " model vdw 1.835 2.520 nonbonded pdb=" O GLN A 516 " pdb=" CD ARG A 520 " model vdw 1.874 3.440 nonbonded pdb=" CB SER A 219 " pdb=" CG2 ILE A 656 " model vdw 1.909 3.860 nonbonded pdb=" OD2 ASP G 10 " pdb=" ND2 ASN G 101 " model vdw 2.006 2.520 ... (remaining 65803 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=0.29 max=1.00 mean=0.99 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.270 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 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 : 0.009 0.068 8625 Z= 0.539 Angle : 1.294 12.617 11764 Z= 0.835 Chirality : 0.057 0.295 1438 Planarity : 0.005 0.055 1537 Dihedral : 9.916 88.595 2721 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 4.97 % Allowed : 7.65 % Favored : 87.38 % Rotamer: Outliers : 1.19 % Allowed : 1.04 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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 (0.30), residues: 750 helix: -1.94 (0.21), residues: 332 sheet: -2.97 (0.56), residues: 68 loop : -0.04 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 164 HIS 0.010 0.003 HIS A 444 PHE 0.019 0.003 PHE A 335 TYR 0.017 0.003 TYR A 453 ARG 0.010 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9238 (m-30) cc_final: 0.9018 (m-30) REVERT: A 84 TRP cc_start: 0.8763 (m100) cc_final: 0.8317 (m-90) REVERT: A 91 ASN cc_start: 0.9134 (m-40) cc_final: 0.8854 (m-40) REVERT: A 325 VAL cc_start: 0.9472 (t) cc_final: 0.9211 (p) REVERT: A 327 PHE cc_start: 0.9148 (m-80) cc_final: 0.8943 (m-80) REVERT: A 401 VAL cc_start: 0.6247 (t) cc_final: 0.6019 (t) REVERT: A 552 GLN cc_start: 0.8863 (pm20) cc_final: 0.8471 (pm20) REVERT: B 173 LEU cc_start: 0.6682 (tt) cc_final: 0.5890 (tt) REVERT: B 176 PHE cc_start: 0.8457 (t80) cc_final: 0.8244 (t80) REVERT: B 202 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6913 (tt) REVERT: B 205 PHE cc_start: 0.6050 (t80) cc_final: 0.5767 (t80) REVERT: B 229 ILE cc_start: 0.9075 (mm) cc_final: 0.8674 (mm) REVERT: B 407 THR cc_start: 0.7762 (t) cc_final: 0.7072 (p) REVERT: B 447 PHE cc_start: 0.7973 (m-10) cc_final: 0.7565 (m-80) outliers start: 8 outliers final: 3 residues processed: 229 average time/residue: 0.2071 time to fit residues: 63.5722 Evaluate side-chains 147 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 216 GLN A 290 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8625 Z= 0.288 Angle : 0.850 11.395 11764 Z= 0.429 Chirality : 0.042 0.288 1438 Planarity : 0.005 0.053 1537 Dihedral : 6.261 31.507 1291 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.40 % Favored : 88.99 % Rotamer: Outliers : 0.59 % Allowed : 4.75 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.29), residues: 750 helix: -0.54 (0.26), residues: 331 sheet: -3.33 (0.44), residues: 84 loop : -1.00 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 164 HIS 0.009 0.002 HIS A 199 PHE 0.030 0.003 PHE G 153 TYR 0.019 0.002 TYR A 467 ARG 0.006 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8646 (pt0) REVERT: A 81 ASP cc_start: 0.9254 (m-30) cc_final: 0.8941 (m-30) REVERT: A 84 TRP cc_start: 0.8639 (m100) cc_final: 0.8280 (m-90) REVERT: A 91 ASN cc_start: 0.9157 (m-40) cc_final: 0.8832 (p0) REVERT: A 111 LEU cc_start: 0.9408 (tt) cc_final: 0.9067 (tt) REVERT: A 213 CYS cc_start: 0.4398 (t) cc_final: 0.1975 (t) REVERT: A 215 MET cc_start: 0.9024 (ttt) cc_final: 0.8676 (ttm) REVERT: A 230 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6557 (t) REVERT: A 231 MET cc_start: 0.8177 (mmm) cc_final: 0.7783 (mmm) REVERT: A 254 TYR cc_start: 0.7825 (m-10) cc_final: 0.7465 (m-10) REVERT: A 277 VAL cc_start: 0.7989 (p) cc_final: 0.7488 (p) REVERT: A 302 PHE cc_start: 0.8621 (m-10) cc_final: 0.8341 (m-80) REVERT: A 325 VAL cc_start: 0.9451 (t) cc_final: 0.9243 (p) REVERT: A 345 TYR cc_start: 0.8619 (t80) cc_final: 0.8337 (t80) REVERT: A 430 PHE cc_start: 0.8270 (m-10) cc_final: 0.7655 (m-80) REVERT: A 453 TYR cc_start: 0.6362 (t80) cc_final: 0.5819 (t80) REVERT: A 501 LEU cc_start: 0.9304 (tp) cc_final: 0.8916 (pp) REVERT: A 552 GLN cc_start: 0.8960 (pm20) cc_final: 0.8651 (pm20) REVERT: B 202 ILE cc_start: 0.7849 (mp) cc_final: 0.7530 (tt) REVERT: B 229 ILE cc_start: 0.9211 (mm) cc_final: 0.8421 (mm) REVERT: B 418 LEU cc_start: 0.8190 (mm) cc_final: 0.7887 (mt) REVERT: B 423 LEU cc_start: 0.7036 (mm) cc_final: 0.6805 (mm) outliers start: 4 outliers final: 0 residues processed: 201 average time/residue: 0.1711 time to fit residues: 48.8151 Evaluate side-chains 141 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 102 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 8625 Z= 0.407 Angle : 0.924 13.141 11764 Z= 0.462 Chirality : 0.043 0.242 1438 Planarity : 0.005 0.051 1537 Dihedral : 6.346 29.595 1291 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 1.48 % Allowed : 11.28 % Favored : 87.25 % Rotamer: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.99 (0.29), residues: 750 helix: -0.50 (0.27), residues: 332 sheet: -3.14 (0.47), residues: 68 loop : -1.68 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 653 HIS 0.009 0.002 HIS A 553 PHE 0.030 0.003 PHE A 181 TYR 0.025 0.003 TYR A 565 ARG 0.014 0.001 ARG G 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9258 (m-30) cc_final: 0.8949 (m-30) REVERT: A 91 ASN cc_start: 0.9237 (m-40) cc_final: 0.8792 (p0) REVERT: A 277 VAL cc_start: 0.7896 (p) cc_final: 0.7197 (p) REVERT: A 343 MET cc_start: 0.9052 (tpt) cc_final: 0.8818 (tmm) REVERT: A 566 VAL cc_start: 0.8607 (t) cc_final: 0.8304 (t) REVERT: B 202 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7795 (tt) REVERT: B 205 PHE cc_start: 0.6399 (t80) cc_final: 0.5533 (t80) REVERT: B 229 ILE cc_start: 0.9211 (mm) cc_final: 0.8042 (mm) outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.1704 time to fit residues: 38.2049 Evaluate side-chains 127 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8625 Z= 0.360 Angle : 0.840 10.592 11764 Z= 0.421 Chirality : 0.041 0.238 1438 Planarity : 0.005 0.053 1537 Dihedral : 6.059 29.573 1291 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 1.48 % Allowed : 10.60 % Favored : 87.92 % Rotamer: Outliers : 0.30 % Allowed : 4.90 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.93 (0.29), residues: 750 helix: -0.36 (0.27), residues: 330 sheet: -3.42 (0.48), residues: 62 loop : -1.71 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 404 HIS 0.005 0.002 HIS A 553 PHE 0.024 0.003 PHE B 177 TYR 0.020 0.002 TYR A 565 ARG 0.008 0.001 ARG G 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9560 (p) cc_final: 0.9083 (p) REVERT: A 84 TRP cc_start: 0.8704 (m100) cc_final: 0.8439 (m-90) REVERT: A 91 ASN cc_start: 0.9251 (m-40) cc_final: 0.9005 (m110) REVERT: A 213 CYS cc_start: 0.4165 (m) cc_final: 0.3142 (m) REVERT: A 277 VAL cc_start: 0.7466 (p) cc_final: 0.6792 (m) REVERT: A 552 GLN cc_start: 0.8936 (pm20) cc_final: 0.8658 (pm20) REVERT: B 82 VAL cc_start: 0.7802 (t) cc_final: 0.7375 (p) REVERT: B 202 ILE cc_start: 0.7949 (mp) cc_final: 0.7705 (tt) REVERT: B 205 PHE cc_start: 0.6488 (t80) cc_final: 0.6275 (t80) REVERT: G 126 TRP cc_start: 0.3630 (m100) cc_final: 0.3419 (m-90) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.1818 time to fit residues: 40.1007 Evaluate side-chains 121 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8625 Z= 0.370 Angle : 0.849 10.560 11764 Z= 0.428 Chirality : 0.042 0.241 1438 Planarity : 0.005 0.057 1537 Dihedral : 6.046 28.266 1291 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.87 % Favored : 87.79 % Rotamer: Outliers : 0.30 % Allowed : 5.50 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.96 (0.29), residues: 750 helix: -0.30 (0.27), residues: 331 sheet: -3.64 (0.46), residues: 70 loop : -1.73 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 164 HIS 0.006 0.002 HIS A 553 PHE 0.025 0.003 PHE B 86 TYR 0.021 0.002 TYR G 161 ARG 0.004 0.001 ARG G 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9371 (p) cc_final: 0.8851 (p) REVERT: A 81 ASP cc_start: 0.9149 (m-30) cc_final: 0.8767 (m-30) REVERT: A 84 TRP cc_start: 0.8807 (m100) cc_final: 0.8505 (m-90) REVERT: A 91 ASN cc_start: 0.9275 (m-40) cc_final: 0.8984 (m110) REVERT: A 213 CYS cc_start: 0.4389 (m) cc_final: 0.3402 (m) REVERT: A 277 VAL cc_start: 0.7992 (p) cc_final: 0.7307 (p) REVERT: A 302 PHE cc_start: 0.9128 (m-80) cc_final: 0.8908 (m-80) REVERT: A 343 MET cc_start: 0.9060 (tpt) cc_final: 0.8649 (tpp) REVERT: A 552 GLN cc_start: 0.9014 (pm20) cc_final: 0.8723 (pm20) REVERT: B 82 VAL cc_start: 0.7873 (t) cc_final: 0.7294 (p) REVERT: B 85 LEU cc_start: 0.8671 (mm) cc_final: 0.8316 (tt) REVERT: B 202 ILE cc_start: 0.8056 (mp) cc_final: 0.7677 (tt) REVERT: B 205 PHE cc_start: 0.6561 (t80) cc_final: 0.5812 (t80) REVERT: B 229 ILE cc_start: 0.9229 (mm) cc_final: 0.8545 (mm) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.1772 time to fit residues: 38.7650 Evaluate side-chains 123 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8625 Z= 0.340 Angle : 0.818 10.560 11764 Z= 0.415 Chirality : 0.042 0.239 1438 Planarity : 0.004 0.051 1537 Dihedral : 5.948 28.819 1291 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.60 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.84 (0.30), residues: 750 helix: -0.07 (0.28), residues: 329 sheet: -3.46 (0.50), residues: 63 loop : -1.87 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 164 HIS 0.005 0.001 HIS A 553 PHE 0.020 0.002 PHE A 218 TYR 0.025 0.002 TYR A 565 ARG 0.003 0.001 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9438 (p) cc_final: 0.9093 (p) REVERT: A 91 ASN cc_start: 0.9226 (m-40) cc_final: 0.9004 (m-40) REVERT: A 213 CYS cc_start: 0.4541 (m) cc_final: 0.3690 (m) REVERT: A 277 VAL cc_start: 0.7766 (p) cc_final: 0.7090 (m) REVERT: A 330 PHE cc_start: 0.7360 (m-80) cc_final: 0.7135 (m-80) REVERT: A 343 MET cc_start: 0.9283 (tpt) cc_final: 0.8858 (tpp) REVERT: A 404 LEU cc_start: 0.3006 (mm) cc_final: 0.2463 (mm) REVERT: A 552 GLN cc_start: 0.9073 (pm20) cc_final: 0.8850 (pm20) REVERT: B 202 ILE cc_start: 0.7932 (mp) cc_final: 0.7649 (tt) REVERT: B 205 PHE cc_start: 0.6574 (t80) cc_final: 0.5680 (t80) REVERT: B 229 ILE cc_start: 0.9302 (mm) cc_final: 0.8612 (mm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1774 time to fit residues: 39.7080 Evaluate side-chains 122 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 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 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8625 Z= 0.233 Angle : 0.746 10.365 11764 Z= 0.377 Chirality : 0.039 0.226 1438 Planarity : 0.004 0.052 1537 Dihedral : 5.567 29.016 1291 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.66 % Favored : 88.99 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.56 (0.30), residues: 750 helix: 0.20 (0.28), residues: 332 sheet: -3.19 (0.54), residues: 62 loop : -1.82 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 164 HIS 0.004 0.001 HIS A 199 PHE 0.021 0.002 PHE B 176 TYR 0.017 0.002 TYR A 565 ARG 0.003 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9090 (m-30) cc_final: 0.8818 (m-30) REVERT: A 91 ASN cc_start: 0.9199 (m-40) cc_final: 0.8987 (m-40) REVERT: A 95 MET cc_start: 0.5677 (ppp) cc_final: 0.5460 (ppp) REVERT: A 213 CYS cc_start: 0.4412 (m) cc_final: 0.3567 (m) REVERT: A 216 GLN cc_start: 0.7648 (tt0) cc_final: 0.7436 (tt0) REVERT: A 231 MET cc_start: 0.7461 (mmp) cc_final: 0.7025 (mmm) REVERT: A 343 MET cc_start: 0.9220 (tpt) cc_final: 0.8875 (tpp) REVERT: A 376 LEU cc_start: 0.8717 (tp) cc_final: 0.6867 (tp) REVERT: A 404 LEU cc_start: 0.2601 (mm) cc_final: 0.2247 (mm) REVERT: A 430 PHE cc_start: 0.7931 (m-10) cc_final: 0.7213 (m-10) REVERT: A 552 GLN cc_start: 0.9068 (pm20) cc_final: 0.8785 (pm20) REVERT: B 82 VAL cc_start: 0.7649 (t) cc_final: 0.7029 (p) REVERT: B 85 LEU cc_start: 0.8536 (mm) cc_final: 0.8259 (tt) REVERT: B 202 ILE cc_start: 0.8081 (mp) cc_final: 0.7643 (tt) REVERT: B 205 PHE cc_start: 0.6238 (t80) cc_final: 0.5591 (t80) REVERT: B 229 ILE cc_start: 0.9252 (mm) cc_final: 0.8442 (mm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1689 time to fit residues: 39.2534 Evaluate side-chains 122 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8625 Z= 0.345 Angle : 0.811 10.552 11764 Z= 0.413 Chirality : 0.041 0.229 1438 Planarity : 0.005 0.056 1537 Dihedral : 5.746 27.784 1291 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.74 % Favored : 87.92 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.71 (0.30), residues: 750 helix: 0.18 (0.28), residues: 330 sheet: -3.26 (0.49), residues: 70 loop : -1.95 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 164 HIS 0.005 0.001 HIS A 553 PHE 0.021 0.003 PHE A 218 TYR 0.014 0.002 TYR B 225 ARG 0.011 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.9225 (m-40) cc_final: 0.9004 (m-40) REVERT: A 213 CYS cc_start: 0.4031 (m) cc_final: 0.2985 (m) REVERT: A 343 MET cc_start: 0.9263 (tpt) cc_final: 0.8934 (tpp) REVERT: A 404 LEU cc_start: 0.2743 (mm) cc_final: 0.2347 (mm) REVERT: A 430 PHE cc_start: 0.8157 (m-10) cc_final: 0.7093 (m-10) REVERT: A 518 VAL cc_start: 0.9322 (t) cc_final: 0.8792 (t) REVERT: B 82 VAL cc_start: 0.7980 (t) cc_final: 0.7435 (p) REVERT: B 202 ILE cc_start: 0.8166 (mp) cc_final: 0.7614 (tt) REVERT: B 227 ILE cc_start: 0.7875 (pt) cc_final: 0.7652 (pt) REVERT: B 229 ILE cc_start: 0.9241 (mm) cc_final: 0.8479 (mm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1717 time to fit residues: 36.8869 Evaluate side-chains 119 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 0.0770 chunk 57 optimal weight: 10.0000 overall best weight: 1.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8625 Z= 0.201 Angle : 0.721 10.261 11764 Z= 0.363 Chirality : 0.039 0.214 1438 Planarity : 0.004 0.053 1537 Dihedral : 5.303 28.118 1291 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.26 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.34 (0.30), residues: 750 helix: 0.48 (0.29), residues: 332 sheet: -2.66 (0.53), residues: 69 loop : -1.88 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 164 HIS 0.004 0.001 HIS A 199 PHE 0.032 0.002 PHE A 181 TYR 0.012 0.001 TYR B 181 ARG 0.004 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.3979 (m) cc_final: 0.3083 (m) REVERT: A 343 MET cc_start: 0.9235 (tpt) cc_final: 0.8873 (tpp) REVERT: A 430 PHE cc_start: 0.7744 (m-10) cc_final: 0.6852 (m-10) REVERT: A 518 VAL cc_start: 0.9183 (t) cc_final: 0.8883 (t) REVERT: A 552 GLN cc_start: 0.9015 (pm20) cc_final: 0.8811 (pm20) REVERT: B 82 VAL cc_start: 0.7812 (t) cc_final: 0.6906 (p) REVERT: B 202 ILE cc_start: 0.8070 (mp) cc_final: 0.7545 (tt) REVERT: B 229 ILE cc_start: 0.9221 (mm) cc_final: 0.8588 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1776 time to fit residues: 38.2262 Evaluate side-chains 123 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 4.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8625 Z= 0.332 Angle : 0.798 10.440 11764 Z= 0.403 Chirality : 0.041 0.218 1438 Planarity : 0.004 0.052 1537 Dihedral : 5.551 27.734 1291 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.47 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.52 (0.30), residues: 750 helix: 0.33 (0.28), residues: 334 sheet: -2.58 (0.50), residues: 72 loop : -2.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 164 HIS 0.006 0.002 HIS A 553 PHE 0.041 0.003 PHE A 181 TYR 0.014 0.002 TYR A 337 ARG 0.009 0.001 ARG A 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9137 (m-30) cc_final: 0.8819 (m-30) REVERT: A 91 ASN cc_start: 0.9321 (m-40) cc_final: 0.9083 (m-40) REVERT: A 213 CYS cc_start: 0.4011 (m) cc_final: 0.3137 (m) REVERT: A 333 GLU cc_start: 0.8830 (tp30) cc_final: 0.8619 (tp30) REVERT: A 343 MET cc_start: 0.8953 (tpt) cc_final: 0.8740 (tpp) REVERT: A 430 PHE cc_start: 0.8028 (m-10) cc_final: 0.6932 (m-10) REVERT: A 518 VAL cc_start: 0.9239 (t) cc_final: 0.8663 (p) REVERT: B 82 VAL cc_start: 0.7830 (t) cc_final: 0.7147 (p) REVERT: B 202 ILE cc_start: 0.8171 (mp) cc_final: 0.7567 (tt) REVERT: B 205 PHE cc_start: 0.5993 (t80) cc_final: 0.5599 (t80) REVERT: B 229 ILE cc_start: 0.9211 (mm) cc_final: 0.8394 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1684 time to fit residues: 34.0252 Evaluate side-chains 117 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.105891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078430 restraints weight = 152461.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078471 restraints weight = 70465.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078988 restraints weight = 40853.764| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8625 Z= 0.300 Angle : 0.778 10.458 11764 Z= 0.392 Chirality : 0.040 0.212 1438 Planarity : 0.004 0.052 1537 Dihedral : 5.532 28.057 1291 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.87 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.51 (0.30), residues: 750 helix: 0.30 (0.28), residues: 336 sheet: -2.48 (0.50), residues: 70 loop : -2.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 164 HIS 0.005 0.001 HIS A 553 PHE 0.035 0.003 PHE B 86 TYR 0.017 0.002 TYR B 225 ARG 0.008 0.001 ARG A 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1568.71 seconds wall clock time: 29 minutes 14.99 seconds (1754.99 seconds total)