Starting phenix.real_space_refine on Wed Feb 14 18:21:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/02_2024/8oe4_16824.pdb" } resolution = 3.6 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= 0.011 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 62 5.16 5 C 6273 2.51 5 N 1682 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 465": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9951 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2388 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1116 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2384 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3957 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 470} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.76, per 1000 atoms: 0.58 Number of scatterers: 9951 At special positions: 0 Unit cell: (104.039, 135.447, 162.929, 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 62 16.00 O 1934 8.00 N 1682 7.00 C 6273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS B 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 115 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 101 " distance=2.02 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 368 " distance=2.04 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 383 " distance=2.04 Simple disulfide: pdb=" SG CYS D 413 " - pdb=" SG CYS D 474 " distance=2.03 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 601 " - " ASN C 81 " " NAG C 602 " - " ASN C 141 " " NAG E 1 " - " ASN A 222 " " NAG F 1 " - " ASN C 180 " Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 2.0 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 28 sheets defined 11.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.735A pdb=" N HIS B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.560A pdb=" N CYS B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.888A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 187 removed outlier: 4.439A pdb=" N LEU B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.583A pdb=" N TRP D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 469 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.101A pdb=" N VAL A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 31 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS A 105 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 33 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 107 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 35 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS A 90 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS A 99 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 88 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.101A pdb=" N VAL A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 31 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS A 105 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 33 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 107 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 35 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 4.753A pdb=" N LEU A 145 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.634A pdb=" N ASN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 190 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 175 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 245 removed outlier: 5.558A pdb=" N ASN A 240 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 257 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 244 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 253 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 279 removed outlier: 3.758A pdb=" N CYS A 274 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 308 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 37 removed outlier: 3.747A pdb=" N HIS C 33 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 removed outlier: 6.461A pdb=" N PHE C 42 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N CYS C 101 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY C 116 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET C 99 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP C 118 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 97 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 100 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 63 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 182 removed outlier: 4.014A pdb=" N ILE C 179 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 141 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE C 219 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 135 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 231 removed outlier: 5.265A pdb=" N ILE C 225 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP C 243 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 280 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 242 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 278 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 272 removed outlier: 3.592A pdb=" N LYS C 268 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 255 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 251 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 54 removed outlier: 4.296A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 92 removed outlier: 5.117A pdb=" N TYR D 88 " --> pdb=" O CYS D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA D 90 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 77 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 92 " --> pdb=" O HIS D 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 92 removed outlier: 5.117A pdb=" N TYR D 88 " --> pdb=" O CYS D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA D 90 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 77 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 92 " --> pdb=" O HIS D 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AC3, first strand: chain 'D' and resid 182 through 189 removed outlier: 3.655A pdb=" N CYS D 186 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL D 170 " --> pdb=" O CYS D 186 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 168 " --> pdb=" O PRO D 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.200A pdb=" N ARG D 242 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 298 through 302 Processing sheet with id=AC6, first strand: chain 'D' and resid 298 through 302 Processing sheet with id=AC7, first strand: chain 'D' and resid 346 through 349 Processing sheet with id=AC8, first strand: chain 'D' and resid 382 through 389 removed outlier: 4.217A pdb=" N TYR D 367 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET D 365 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 412 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA D 420 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR D 432 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 450 through 458 removed outlier: 5.874A pdb=" N HIS D 451 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 467 " --> pdb=" O HIS D 451 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER D 461 " --> pdb=" O HIS D 457 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 493 through 498 399 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 4.48 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: 3202 1.34 - 1.47: 2530 1.47 - 1.59: 4394 1.59 - 1.71: 1 1.71 - 1.83: 78 Bond restraints: 10205 Sorted by residual: bond pdb=" CG PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.503 1.311 0.192 3.40e-02 8.65e+02 3.21e+01 bond pdb=" CB PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.29e+01 bond pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 1.465 1.447 0.018 1.11e-02 8.12e+03 2.62e+00 ... (remaining 10200 not shown) Histogram of bond angle deviations from ideal: 91.36 - 100.82: 10 100.82 - 110.27: 2513 110.27 - 119.73: 6389 119.73 - 129.18: 4871 129.18 - 138.64: 109 Bond angle restraints: 13892 Sorted by residual: angle pdb=" CA PRO A 326 " pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO A 326 " pdb=" CD PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 103.20 91.36 11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 104.50 95.89 8.61 1.90e+00 2.77e-01 2.06e+01 angle pdb=" N PRO A 326 " pdb=" CA PRO A 326 " pdb=" C PRO A 326 " ideal model delta sigma weight residual 112.01 120.10 -8.09 1.84e+00 2.95e-01 1.93e+01 angle pdb=" C ASN C 81 " pdb=" CA ASN C 81 " pdb=" CB ASN C 81 " ideal model delta sigma weight residual 110.43 116.93 -6.50 1.68e+00 3.54e-01 1.50e+01 ... (remaining 13887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 5789 21.28 - 42.55: 385 42.55 - 63.83: 49 63.83 - 85.10: 15 85.10 - 106.38: 9 Dihedral angle restraints: 6247 sinusoidal: 2605 harmonic: 3642 Sorted by residual: dihedral pdb=" CB CYS D 24 " pdb=" SG CYS D 24 " pdb=" SG CYS D 30 " pdb=" CB CYS D 30 " ideal model delta sinusoidal sigma weight residual 93.00 153.18 -60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASN C 141 " pdb=" C ASN C 141 " pdb=" N MET C 142 " pdb=" CA MET C 142 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual -86.00 -129.31 43.31 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1261 0.062 - 0.124: 253 0.124 - 0.186: 22 0.186 - 0.248: 5 0.248 - 0.310: 1 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA PRO A 326 " pdb=" N PRO A 326 " pdb=" C PRO A 326 " pdb=" CB PRO A 326 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 222 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1539 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 81 " 0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN C 81 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 81 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 81 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 325 " -0.056 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 326 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " -0.027 2.00e-02 2.50e+03 2.53e-02 7.98e+00 pdb=" CG ASN A 222 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.025 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 664 2.74 - 3.28: 8931 3.28 - 3.82: 15796 3.82 - 4.36: 18796 4.36 - 4.90: 32359 Nonbonded interactions: 76546 Sorted by model distance: nonbonded pdb=" OD1 ASN A 135 " pdb=" OG SER A 137 " model vdw 2.196 2.440 nonbonded pdb=" O ASP A 84 " pdb=" OH TYR A 88 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR B 100 " pdb=" OG SER B 168 " model vdw 2.254 2.440 nonbonded pdb=" OG SER A 158 " pdb=" O GLU A 209 " model vdw 2.281 2.440 nonbonded pdb=" OE2 GLU B 101 " pdb=" OG SER B 132 " model vdw 2.285 2.440 ... (remaining 76541 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: 2.230 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: 7.790 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.830 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.005 0.192 10205 Z= 0.366 Angle : 0.848 16.562 13892 Z= 0.468 Chirality : 0.049 0.310 1542 Planarity : 0.006 0.098 1777 Dihedral : 14.527 106.377 3835 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.73 % Allowed : 12.74 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.38 (0.23), residues: 1231 helix: -0.14 (0.49), residues: 99 sheet: 0.21 (0.22), residues: 520 loop : -0.61 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 466 HIS 0.018 0.001 HIS D 438 PHE 0.026 0.002 PHE D 208 TYR 0.035 0.003 TYR D 357 ARG 0.022 0.001 ARG D 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8972 (tpp) cc_final: 0.8174 (tpp) REVERT: B 107 ASP cc_start: 0.9073 (p0) cc_final: 0.8549 (t0) REVERT: C 99 MET cc_start: 0.8464 (mmm) cc_final: 0.7499 (mmt) REVERT: C 184 ASP cc_start: 0.9244 (m-30) cc_final: 0.8527 (t0) REVERT: D 136 SER cc_start: 0.8247 (m) cc_final: 0.7954 (t) REVERT: D 143 LEU cc_start: 0.8429 (mt) cc_final: 0.8061 (pp) REVERT: D 408 MET cc_start: 0.6375 (mtt) cc_final: 0.2816 (tmm) outliers start: 8 outliers final: 3 residues processed: 121 average time/residue: 0.2789 time to fit residues: 45.6937 Evaluate side-chains 63 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 247 GLN D 339 HIS D 438 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10205 Z= 0.250 Angle : 0.642 10.364 13892 Z= 0.327 Chirality : 0.045 0.163 1542 Planarity : 0.004 0.063 1777 Dihedral : 7.631 72.034 1513 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.38 % Allowed : 16.32 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.15 (0.23), residues: 1231 helix: 0.93 (0.52), residues: 98 sheet: 0.31 (0.21), residues: 525 loop : -0.57 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 45 HIS 0.006 0.001 HIS D 438 PHE 0.026 0.001 PHE C 75 TYR 0.021 0.002 TYR D 357 ARG 0.006 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8483 (tpp) cc_final: 0.8183 (tpp) REVERT: A 270 SER cc_start: 0.9470 (OUTLIER) cc_final: 0.8863 (p) REVERT: B 39 LYS cc_start: 0.8653 (tttp) cc_final: 0.8285 (mtmm) REVERT: B 107 ASP cc_start: 0.9102 (p0) cc_final: 0.8534 (t0) REVERT: C 99 MET cc_start: 0.8565 (mmm) cc_final: 0.7756 (mmt) REVERT: C 184 ASP cc_start: 0.9259 (m-30) cc_final: 0.8644 (t0) REVERT: D 136 SER cc_start: 0.8291 (m) cc_final: 0.7976 (t) REVERT: D 143 LEU cc_start: 0.8304 (mt) cc_final: 0.7953 (pp) REVERT: D 256 LEU cc_start: 0.8985 (tp) cc_final: 0.8737 (tt) REVERT: D 408 MET cc_start: 0.6346 (mtt) cc_final: 0.3329 (tmm) outliers start: 26 outliers final: 17 residues processed: 87 average time/residue: 0.2281 time to fit residues: 28.4648 Evaluate side-chains 75 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 50.0000 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 overall best weight: 2.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS D 287 HIS D 330 GLN D 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10205 Z= 0.341 Angle : 0.672 10.880 13892 Z= 0.341 Chirality : 0.045 0.150 1542 Planarity : 0.005 0.052 1777 Dihedral : 6.833 58.861 1510 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.76 % Allowed : 16.13 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.11 (0.24), residues: 1231 helix: 0.88 (0.51), residues: 104 sheet: 0.31 (0.22), residues: 540 loop : -0.53 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 45 HIS 0.007 0.001 HIS D 339 PHE 0.010 0.002 PHE D 99 TYR 0.019 0.002 TYR C 136 ARG 0.006 0.001 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 56 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8457 (tpp) cc_final: 0.8183 (tpp) REVERT: A 250 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7848 (ttt90) REVERT: A 270 SER cc_start: 0.9508 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 39 LYS cc_start: 0.8699 (tttp) cc_final: 0.8339 (mtmm) REVERT: B 107 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8597 (t0) REVERT: C 34 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (pt) REVERT: C 41 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7483 (tp) REVERT: C 44 MET cc_start: 0.7644 (tpp) cc_final: 0.7349 (mmm) REVERT: C 65 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: C 99 MET cc_start: 0.8733 (mmm) cc_final: 0.7843 (mmt) REVERT: C 184 ASP cc_start: 0.9251 (m-30) cc_final: 0.8702 (t0) REVERT: D 136 SER cc_start: 0.8418 (m) cc_final: 0.8099 (t) REVERT: D 143 LEU cc_start: 0.8338 (mt) cc_final: 0.7936 (pp) REVERT: D 256 LEU cc_start: 0.8941 (tp) cc_final: 0.8389 (pp) REVERT: D 408 MET cc_start: 0.6095 (mtt) cc_final: 0.3371 (tmm) outliers start: 41 outliers final: 28 residues processed: 90 average time/residue: 0.2139 time to fit residues: 28.3716 Evaluate side-chains 86 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 52 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10205 Z= 0.369 Angle : 0.671 12.743 13892 Z= 0.339 Chirality : 0.045 0.160 1542 Planarity : 0.004 0.048 1777 Dihedral : 5.933 57.530 1510 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.31 % Allowed : 16.50 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.27 (0.24), residues: 1231 helix: 0.81 (0.52), residues: 101 sheet: 0.19 (0.22), residues: 548 loop : -0.64 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 466 HIS 0.010 0.001 HIS D 339 PHE 0.011 0.002 PHE D 439 TYR 0.024 0.002 TYR D 357 ARG 0.005 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 55 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8422 (tpp) cc_final: 0.8152 (tpp) REVERT: A 270 SER cc_start: 0.9496 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 39 LYS cc_start: 0.8709 (tttp) cc_final: 0.8357 (mtmm) REVERT: B 107 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8662 (t0) REVERT: C 34 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8337 (pt) REVERT: C 65 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6540 (t-90) REVERT: C 99 MET cc_start: 0.8733 (mmm) cc_final: 0.7753 (mmt) REVERT: C 142 MET cc_start: 0.8932 (mpp) cc_final: 0.8605 (mpp) REVERT: C 184 ASP cc_start: 0.9280 (m-30) cc_final: 0.8674 (t0) REVERT: D 136 SER cc_start: 0.8468 (m) cc_final: 0.8154 (t) REVERT: D 143 LEU cc_start: 0.8241 (mt) cc_final: 0.7834 (pp) REVERT: D 256 LEU cc_start: 0.8915 (tp) cc_final: 0.8425 (pp) REVERT: D 408 MET cc_start: 0.6274 (mtt) cc_final: 0.3785 (tmm) outliers start: 47 outliers final: 31 residues processed: 95 average time/residue: 0.2043 time to fit residues: 28.8073 Evaluate side-chains 88 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 53 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 102 optimal weight: 30.0000 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10205 Z= 0.229 Angle : 0.594 12.565 13892 Z= 0.299 Chirality : 0.043 0.183 1542 Planarity : 0.004 0.043 1777 Dihedral : 5.661 58.969 1510 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.57 % Allowed : 18.06 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.11 (0.24), residues: 1231 helix: 1.16 (0.52), residues: 104 sheet: 0.26 (0.22), residues: 531 loop : -0.54 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 401 HIS 0.004 0.001 HIS C 65 PHE 0.012 0.001 PHE A 140 TYR 0.017 0.001 TYR D 357 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 55 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8419 (tpp) cc_final: 0.8125 (tpp) REVERT: A 270 SER cc_start: 0.9509 (m) cc_final: 0.8912 (p) REVERT: B 39 LYS cc_start: 0.8707 (tttp) cc_final: 0.8351 (mtmm) REVERT: B 107 ASP cc_start: 0.9055 (p0) cc_final: 0.8655 (t0) REVERT: C 65 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6601 (t-90) REVERT: C 99 MET cc_start: 0.8728 (mmm) cc_final: 0.7775 (mmt) REVERT: C 142 MET cc_start: 0.8997 (mpp) cc_final: 0.8759 (mpp) REVERT: C 184 ASP cc_start: 0.9342 (m-30) cc_final: 0.8733 (t0) REVERT: C 186 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7660 (mm) REVERT: D 136 SER cc_start: 0.8406 (m) cc_final: 0.8115 (t) REVERT: D 143 LEU cc_start: 0.8257 (mt) cc_final: 0.7861 (pp) REVERT: D 356 MET cc_start: 0.7888 (mtm) cc_final: 0.7575 (mmm) REVERT: D 408 MET cc_start: 0.6183 (mtt) cc_final: 0.3589 (tmm) outliers start: 39 outliers final: 28 residues processed: 90 average time/residue: 0.2022 time to fit residues: 27.0777 Evaluate side-chains 82 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 52 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 30.0000 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10205 Z= 0.162 Angle : 0.561 9.386 13892 Z= 0.279 Chirality : 0.042 0.148 1542 Planarity : 0.004 0.043 1777 Dihedral : 5.212 56.680 1510 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.75 % Allowed : 19.52 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.04 (0.24), residues: 1231 helix: 1.18 (0.52), residues: 110 sheet: 0.39 (0.22), residues: 525 loop : -0.46 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.004 0.001 HIS B 94 PHE 0.013 0.001 PHE A 140 TYR 0.014 0.001 TYR D 357 ARG 0.007 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 45 MET cc_start: 0.8387 (tpp) cc_final: 0.8073 (tpp) REVERT: A 270 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.8960 (p) REVERT: B 39 LYS cc_start: 0.8699 (tttp) cc_final: 0.8404 (mtmm) REVERT: B 107 ASP cc_start: 0.9029 (p0) cc_final: 0.8626 (t0) REVERT: C 34 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (pt) REVERT: C 41 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7126 (mm) REVERT: C 44 MET cc_start: 0.7994 (mmm) cc_final: 0.7697 (mmm) REVERT: C 65 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6668 (t-90) REVERT: C 99 MET cc_start: 0.8732 (mmm) cc_final: 0.7816 (mmt) REVERT: C 142 MET cc_start: 0.8928 (mpp) cc_final: 0.8508 (mpp) REVERT: C 184 ASP cc_start: 0.9310 (m-30) cc_final: 0.8723 (t0) REVERT: C 186 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7704 (mm) REVERT: D 136 SER cc_start: 0.8306 (m) cc_final: 0.8039 (t) REVERT: D 143 LEU cc_start: 0.8337 (mt) cc_final: 0.7925 (pp) REVERT: D 408 MET cc_start: 0.6204 (mtt) cc_final: 0.3719 (tmm) outliers start: 30 outliers final: 19 residues processed: 81 average time/residue: 0.2096 time to fit residues: 25.2809 Evaluate side-chains 75 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10205 Z= 0.311 Angle : 0.637 13.362 13892 Z= 0.318 Chirality : 0.043 0.147 1542 Planarity : 0.004 0.043 1777 Dihedral : 5.651 59.498 1510 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.67 % Allowed : 19.25 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.08 (0.24), residues: 1231 helix: 1.26 (0.53), residues: 101 sheet: 0.31 (0.22), residues: 514 loop : -0.53 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 45 HIS 0.005 0.001 HIS C 65 PHE 0.013 0.002 PHE B 109 TYR 0.017 0.002 TYR D 36 ARG 0.006 0.001 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 53 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: A 45 MET cc_start: 0.8358 (tpp) cc_final: 0.8029 (tpp) REVERT: A 270 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.8872 (p) REVERT: B 39 LYS cc_start: 0.8723 (tttp) cc_final: 0.8424 (mtmm) REVERT: B 107 ASP cc_start: 0.9079 (p0) cc_final: 0.8651 (t0) REVERT: C 65 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6488 (t-90) REVERT: C 99 MET cc_start: 0.8707 (mmm) cc_final: 0.7752 (mmt) REVERT: C 142 MET cc_start: 0.9179 (mpp) cc_final: 0.8804 (mpp) REVERT: C 184 ASP cc_start: 0.9328 (m-30) cc_final: 0.8722 (t0) REVERT: C 186 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7731 (mm) REVERT: D 136 SER cc_start: 0.8420 (m) cc_final: 0.8119 (t) REVERT: D 143 LEU cc_start: 0.8326 (mt) cc_final: 0.7846 (pp) REVERT: D 356 MET cc_start: 0.7755 (mtm) cc_final: 0.7241 (pmm) REVERT: D 408 MET cc_start: 0.6279 (mtt) cc_final: 0.2363 (tmm) outliers start: 40 outliers final: 29 residues processed: 87 average time/residue: 0.2143 time to fit residues: 27.3153 Evaluate side-chains 83 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 50 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 518 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.0060 chunk 108 optimal weight: 30.0000 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10205 Z= 0.153 Angle : 0.568 9.416 13892 Z= 0.283 Chirality : 0.042 0.141 1542 Planarity : 0.004 0.041 1777 Dihedral : 5.193 55.617 1510 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.38 % Allowed : 20.62 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.12 (0.25), residues: 1231 helix: 1.51 (0.53), residues: 104 sheet: 0.36 (0.22), residues: 524 loop : -0.35 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 401 HIS 0.003 0.001 HIS C 161 PHE 0.013 0.001 PHE A 140 TYR 0.016 0.001 TYR D 357 ARG 0.006 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 53 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8376 (tpp) cc_final: 0.8040 (tpp) REVERT: A 211 MET cc_start: 0.8039 (mpp) cc_final: 0.7752 (mpp) REVERT: A 270 SER cc_start: 0.9508 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 39 LYS cc_start: 0.8706 (tttp) cc_final: 0.8407 (mtmm) REVERT: B 107 ASP cc_start: 0.9020 (p0) cc_final: 0.8652 (t0) REVERT: C 34 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8057 (pt) REVERT: C 65 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6605 (t-90) REVERT: C 99 MET cc_start: 0.8670 (mmm) cc_final: 0.7760 (mmt) REVERT: C 142 MET cc_start: 0.9151 (mpp) cc_final: 0.8677 (mpp) REVERT: C 184 ASP cc_start: 0.9293 (m-30) cc_final: 0.8707 (t0) REVERT: C 186 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7686 (mm) REVERT: D 136 SER cc_start: 0.8304 (m) cc_final: 0.8043 (t) REVERT: D 143 LEU cc_start: 0.8228 (mt) cc_final: 0.7844 (pp) REVERT: D 408 MET cc_start: 0.6278 (mtt) cc_final: 0.3149 (tmm) outliers start: 26 outliers final: 20 residues processed: 75 average time/residue: 0.2120 time to fit residues: 23.6470 Evaluate side-chains 75 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10205 Z= 0.451 Angle : 0.709 9.015 13892 Z= 0.357 Chirality : 0.045 0.146 1542 Planarity : 0.005 0.041 1777 Dihedral : 5.993 59.363 1510 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 2.47 % Allowed : 20.71 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.27 (0.24), residues: 1231 helix: 0.56 (0.51), residues: 101 sheet: 0.21 (0.22), residues: 528 loop : -0.59 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 45 HIS 0.007 0.001 HIS C 65 PHE 0.018 0.002 PHE B 109 TYR 0.020 0.002 TYR D 36 ARG 0.008 0.001 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 49 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8375 (tpp) cc_final: 0.8040 (tpp) REVERT: A 270 SER cc_start: 0.9431 (m) cc_final: 0.8780 (p) REVERT: B 39 LYS cc_start: 0.8700 (tttp) cc_final: 0.8358 (mtmm) REVERT: B 107 ASP cc_start: 0.9141 (p0) cc_final: 0.8690 (t0) REVERT: C 99 MET cc_start: 0.8700 (mmm) cc_final: 0.7757 (mmt) REVERT: C 142 MET cc_start: 0.9149 (mpp) cc_final: 0.8648 (mpp) REVERT: C 184 ASP cc_start: 0.9365 (OUTLIER) cc_final: 0.8759 (t0) REVERT: C 186 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7755 (mm) REVERT: D 136 SER cc_start: 0.8448 (m) cc_final: 0.8076 (p) REVERT: D 143 LEU cc_start: 0.8272 (mt) cc_final: 0.7799 (pp) REVERT: D 356 MET cc_start: 0.7763 (mtm) cc_final: 0.7372 (mpp) REVERT: D 408 MET cc_start: 0.6359 (mtt) cc_final: 0.3285 (tmm) outliers start: 27 outliers final: 24 residues processed: 70 average time/residue: 0.2093 time to fit residues: 22.1692 Evaluate side-chains 75 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 49 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 40.0000 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10205 Z= 0.307 Angle : 0.621 9.601 13892 Z= 0.313 Chirality : 0.043 0.152 1542 Planarity : 0.004 0.044 1777 Dihedral : 5.726 58.529 1510 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.84 % Allowed : 20.53 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.30 (0.24), residues: 1231 helix: 0.72 (0.52), residues: 101 sheet: 0.14 (0.22), residues: 532 loop : -0.60 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 466 HIS 0.004 0.001 HIS C 65 PHE 0.012 0.002 PHE B 109 TYR 0.021 0.002 TYR D 282 ARG 0.008 0.001 ARG C 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 49 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8366 (tpp) cc_final: 0.8004 (tpp) REVERT: A 120 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: A 270 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.8811 (p) REVERT: B 39 LYS cc_start: 0.8707 (tttp) cc_final: 0.8424 (mtmm) REVERT: B 107 ASP cc_start: 0.9105 (p0) cc_final: 0.8637 (t0) REVERT: C 99 MET cc_start: 0.8672 (mmm) cc_final: 0.7754 (mmt) REVERT: C 142 MET cc_start: 0.9151 (mpp) cc_final: 0.8674 (mpp) REVERT: C 184 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.8778 (t0) REVERT: C 186 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7724 (mm) REVERT: D 136 SER cc_start: 0.8468 (m) cc_final: 0.8163 (t) REVERT: D 143 LEU cc_start: 0.8332 (mt) cc_final: 0.7927 (pp) REVERT: D 356 MET cc_start: 0.7779 (mtm) cc_final: 0.7290 (mpp) REVERT: D 396 MET cc_start: 0.3506 (tmm) cc_final: 0.2691 (ttt) REVERT: D 408 MET cc_start: 0.6288 (mtt) cc_final: 0.3427 (tmm) outliers start: 31 outliers final: 26 residues processed: 74 average time/residue: 0.2077 time to fit residues: 23.2188 Evaluate side-chains 78 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 48 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 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 = 0.4207 r_free = 0.4207 target = 0.101666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070870 restraints weight = 50433.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.068788 restraints weight = 31506.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068805 restraints weight = 25409.725| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10205 Z= 0.206 Angle : 0.569 8.819 13892 Z= 0.285 Chirality : 0.042 0.145 1542 Planarity : 0.004 0.044 1777 Dihedral : 5.308 55.464 1510 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 2.75 % Allowed : 20.71 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.15 (0.25), residues: 1231 helix: 1.06 (0.53), residues: 101 sheet: 0.18 (0.22), residues: 530 loop : -0.47 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 466 HIS 0.003 0.001 HIS C 161 PHE 0.012 0.001 PHE A 140 TYR 0.022 0.001 TYR D 282 ARG 0.007 0.000 ARG C 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.80 seconds wall clock time: 37 minutes 3.17 seconds (2223.17 seconds total)