Starting phenix.real_space_refine on Mon Mar 11 11:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/03_2024/7y1t_33572.pdb" } resolution = 3.24 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= 0.047 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 1 7.51 5 S 38 5.16 5 C 5127 2.51 5 N 1357 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 140": "OE1" <-> "OE2" 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: 8112 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4114 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 507} Chain breaks: 3 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2714 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1038 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Chain: "E" 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: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.63 Number of scatterers: 8112 At special positions: 0 Unit cell: (100.225, 75.96, 150.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 Ca 5 19.99 S 38 16.00 O 1584 8.00 N 1357 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS B 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " 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 G 3 " - " MAN G 6 " ALPHA1-4 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " MAN G 4 " - " MAN G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 701 " - " ASN A 525 " " NAG B 501 " - " ASN B 389 " " NAG B 502 " - " ASN B 191 " " NAG B 503 " - " ASN B 360 " " NAG C 1 " - " ASN A 260 " " NAG D 401 " - " ASN D 107 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 414 " " NAG G 1 " - " ASN A 266 " Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 14.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.459A pdb=" N GLY A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.609A pdb=" N THR A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.816A pdb=" N HIS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 126 through 136 removed outlier: 3.985A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.770A pdb=" N HIS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.083A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 330 through 345 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.989A pdb=" N LEU D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.020A pdb=" N SER D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.921A pdb=" N ASP A 422 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 412 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 408 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 4.016A pdb=" N ALA A 81 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 4.046A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.958A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.754A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283 removed outlier: 4.020A pdb=" N SER A 279 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 6.330A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.737A pdb=" N GLU A 537 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 478 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 476 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 529 removed outlier: 4.043A pdb=" N LYS A 524 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 496 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 528 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 492 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.669A pdb=" N HIS B 422 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 407 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 409 " --> pdb=" O GLN B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 393 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 189 removed outlier: 6.411A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 146 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 109 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 111 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 149 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 296 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.052A pdb=" N PHE D 228 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 127 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 106 removed outlier: 3.746A pdb=" N ILE D 102 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 190 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 104 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY D 187 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 144 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 139 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 156 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 141 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER D 154 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN D 143 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR D 152 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR D 145 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP D 150 " --> pdb=" O TYR D 145 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 594 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: 2.28 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2645 1.34 - 1.46: 1943 1.46 - 1.58: 3630 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 8278 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 MAN G 6 " pdb=" C2 MAN G 6 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 8273 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 238 106.54 - 113.41: 4496 113.41 - 120.27: 2751 120.27 - 127.13: 3665 127.13 - 133.99: 80 Bond angle restraints: 11230 Sorted by residual: angle pdb=" C ASP A 288 " pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 124.31 130.49 -6.18 1.67e+00 3.59e-01 1.37e+01 angle pdb=" C SER A 201 " pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.80e+00 angle pdb=" CA ASP A 289 " pdb=" CB ASP A 289 " pdb=" CG ASP A 289 " ideal model delta sigma weight residual 112.60 114.90 -2.30 1.00e+00 1.00e+00 5.27e+00 angle pdb=" CA CYS B 259 " pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " ideal model delta sigma weight residual 114.40 119.52 -5.12 2.30e+00 1.89e-01 4.96e+00 angle pdb=" C PHE B 195 " pdb=" N GLU B 196 " pdb=" CA GLU B 196 " ideal model delta sigma weight residual 120.31 117.19 3.12 1.52e+00 4.33e-01 4.21e+00 ... (remaining 11225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 4778 22.77 - 45.55: 283 45.55 - 68.32: 58 68.32 - 91.10: 20 91.10 - 113.87: 19 Dihedral angle restraints: 5158 sinusoidal: 2207 harmonic: 2951 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -38.55 -47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CB CYS A 401 " pdb=" SG CYS A 401 " pdb=" SG CYS B 259 " pdb=" CB CYS B 259 " ideal model delta sinusoidal sigma weight residual -86.00 -126.14 40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ALA B 329 " pdb=" C ALA B 329 " pdb=" N ASN B 330 " pdb=" CA ASN B 330 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1286 0.316 - 0.633: 2 0.633 - 0.949: 1 0.949 - 1.266: 0 1.266 - 1.582: 3 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.47e+02 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 266 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 414 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.28e+01 ... (remaining 1289 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 266 " -0.163 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" CG ASN A 266 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 266 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 266 " 0.340 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.248 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 414 " -0.152 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN B 414 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 414 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 414 " 0.325 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 525 " -0.115 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" CG ASN A 525 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 525 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 525 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.163 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 88 2.58 - 3.16: 6368 3.16 - 3.74: 11799 3.74 - 4.32: 16459 4.32 - 4.90: 27765 Nonbonded interactions: 62479 Sorted by model distance: nonbonded pdb=" OD1 ASP D 217 " pdb="MN MN B 505 " model vdw 1.998 2.320 nonbonded pdb=" OG SER A 144 " pdb=" OD1 ASP A 146 " model vdw 2.130 2.440 nonbonded pdb=" NZ LYS B 327 " pdb=" O ALA B 329 " model vdw 2.182 2.520 nonbonded pdb=" OD1 ASP B 130 " pdb=" ND2 ASN B 332 " model vdw 2.190 2.520 nonbonded pdb=" OD1 ASP A 24 " pdb=" N PHE A 25 " model vdw 2.233 2.520 ... (remaining 62474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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 individual isotropic 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: 3.220 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: 0.000 Extract box with map and model: 12.050 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8278 Z= 0.214 Angle : 0.588 6.573 11230 Z= 0.277 Chirality : 0.087 1.582 1292 Planarity : 0.004 0.104 1449 Dihedral : 16.885 113.873 3244 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.27), residues: 1014 helix: 1.39 (0.57), residues: 98 sheet: 0.21 (0.29), residues: 337 loop : -1.33 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.002 0.000 HIS A 113 PHE 0.017 0.001 PHE B 137 TYR 0.011 0.001 TYR A 200 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 474 PHE cc_start: 0.3816 (p90) cc_final: 0.3565 (p90) REVERT: B 250 LEU cc_start: 0.8421 (mt) cc_final: 0.8081 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2049 time to fit residues: 35.6300 Evaluate side-chains 87 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8278 Z= 0.237 Angle : 0.635 9.269 11230 Z= 0.304 Chirality : 0.047 0.277 1292 Planarity : 0.004 0.074 1449 Dihedral : 12.275 95.723 1472 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.22 % Allowed : 10.95 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.67 (0.27), residues: 1014 helix: 1.78 (0.57), residues: 100 sheet: 0.02 (0.27), residues: 373 loop : -1.23 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.003 0.001 HIS D 138 PHE 0.028 0.002 PHE B 137 TYR 0.014 0.001 TYR A 178 ARG 0.004 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 PHE cc_start: 0.3624 (p90) cc_final: 0.3412 (p90) REVERT: A 561 GLU cc_start: 0.7055 (tp30) cc_final: 0.6737 (tp30) REVERT: B 224 CYS cc_start: 0.6287 (m) cc_final: 0.6062 (m) REVERT: B 278 MET cc_start: 0.7389 (ptp) cc_final: 0.7064 (ptp) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.1868 time to fit residues: 25.7853 Evaluate side-chains 84 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 377 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN B 353 GLN B 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8278 Z= 0.348 Angle : 0.688 15.428 11230 Z= 0.338 Chirality : 0.050 0.335 1292 Planarity : 0.004 0.059 1449 Dihedral : 10.565 93.209 1472 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.68 % Allowed : 14.36 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.90 (0.27), residues: 1014 helix: 1.51 (0.57), residues: 100 sheet: -0.22 (0.27), residues: 374 loop : -1.27 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.024 0.002 PHE B 137 TYR 0.023 0.002 TYR A 275 ARG 0.004 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 224 CYS cc_start: 0.6296 (m) cc_final: 0.6023 (m) REVERT: B 278 MET cc_start: 0.7661 (ptp) cc_final: 0.7440 (ptp) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 0.2034 time to fit residues: 27.4760 Evaluate side-chains 87 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN B 353 GLN B 404 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8278 Z= 0.231 Angle : 0.617 13.873 11230 Z= 0.298 Chirality : 0.047 0.309 1292 Planarity : 0.004 0.042 1449 Dihedral : 10.008 92.875 1472 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.07 % Allowed : 16.79 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.89 (0.27), residues: 1014 helix: 1.37 (0.56), residues: 102 sheet: -0.29 (0.27), residues: 373 loop : -1.19 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.022 0.001 PHE B 137 TYR 0.012 0.001 TYR A 275 ARG 0.002 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7878 (t0) cc_final: 0.7611 (t0) REVERT: B 278 MET cc_start: 0.7580 (ptp) cc_final: 0.7311 (ptp) outliers start: 17 outliers final: 16 residues processed: 92 average time/residue: 0.2059 time to fit residues: 26.4743 Evaluate side-chains 89 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8278 Z= 0.193 Angle : 0.590 11.899 11230 Z= 0.283 Chirality : 0.046 0.303 1292 Planarity : 0.004 0.040 1449 Dihedral : 9.622 91.897 1472 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.31 % Allowed : 17.64 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.79 (0.27), residues: 1014 helix: 1.52 (0.56), residues: 102 sheet: -0.23 (0.27), residues: 373 loop : -1.13 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.019 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7765 (t0) cc_final: 0.7493 (t0) REVERT: B 103 TYR cc_start: 0.8211 (m-10) cc_final: 0.7917 (m-80) REVERT: B 278 MET cc_start: 0.7503 (ptp) cc_final: 0.7255 (ptp) outliers start: 19 outliers final: 17 residues processed: 92 average time/residue: 0.1944 time to fit residues: 25.5898 Evaluate side-chains 90 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8278 Z= 0.449 Angle : 0.716 11.993 11230 Z= 0.356 Chirality : 0.050 0.314 1292 Planarity : 0.004 0.039 1449 Dihedral : 9.754 89.757 1472 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.65 % Allowed : 18.13 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -0.98 (0.27), residues: 1014 helix: 1.16 (0.56), residues: 102 sheet: -0.33 (0.27), residues: 373 loop : -1.23 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 61 HIS 0.005 0.001 HIS B 307 PHE 0.028 0.002 PHE B 137 TYR 0.022 0.002 TYR A 275 ARG 0.004 0.001 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 0.952 Fit side-chains REVERT: A 275 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 368 ASP cc_start: 0.7947 (t0) cc_final: 0.7696 (t0) REVERT: D 140 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6014 (tp30) outliers start: 30 outliers final: 21 residues processed: 99 average time/residue: 0.1921 time to fit residues: 27.0739 Evaluate side-chains 94 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8278 Z= 0.239 Angle : 0.625 12.263 11230 Z= 0.305 Chirality : 0.047 0.299 1292 Planarity : 0.004 0.042 1449 Dihedral : 9.439 91.123 1472 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.92 % Allowed : 19.22 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.86 (0.27), residues: 1014 helix: 1.26 (0.56), residues: 103 sheet: -0.26 (0.27), residues: 372 loop : -1.15 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.028 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 368 ASP cc_start: 0.7950 (t0) cc_final: 0.7674 (t0) REVERT: A 409 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8103 (ptp) REVERT: D 140 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5942 (tp30) outliers start: 24 outliers final: 18 residues processed: 93 average time/residue: 0.2715 time to fit residues: 36.1711 Evaluate side-chains 92 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8278 Z= 0.247 Angle : 0.621 11.531 11230 Z= 0.302 Chirality : 0.047 0.298 1292 Planarity : 0.004 0.042 1449 Dihedral : 9.268 89.997 1472 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.28 % Allowed : 19.22 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.83 (0.27), residues: 1014 helix: 1.33 (0.56), residues: 103 sheet: -0.26 (0.27), residues: 372 loop : -1.12 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.027 0.001 PHE B 137 TYR 0.011 0.001 TYR A 275 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 368 ASP cc_start: 0.7993 (t0) cc_final: 0.7712 (t0) REVERT: A 409 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: D 140 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6123 (tp30) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1920 time to fit residues: 25.6854 Evaluate side-chains 96 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8278 Z= 0.180 Angle : 0.593 10.132 11230 Z= 0.286 Chirality : 0.046 0.294 1292 Planarity : 0.004 0.044 1449 Dihedral : 8.929 88.506 1472 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.43 % Allowed : 19.95 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.74 (0.27), residues: 1014 helix: 1.46 (0.56), residues: 103 sheet: -0.19 (0.27), residues: 372 loop : -1.08 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.025 0.001 PHE B 137 TYR 0.010 0.001 TYR A 562 ARG 0.002 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 368 ASP cc_start: 0.8029 (t0) cc_final: 0.7752 (t0) REVERT: D 140 GLU cc_start: 0.6273 (tp30) cc_final: 0.6058 (tp30) outliers start: 20 outliers final: 17 residues processed: 93 average time/residue: 0.2046 time to fit residues: 26.7113 Evaluate side-chains 90 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8278 Z= 0.252 Angle : 0.615 10.200 11230 Z= 0.298 Chirality : 0.047 0.296 1292 Planarity : 0.004 0.043 1449 Dihedral : 8.879 86.721 1472 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.80 % Allowed : 19.59 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.73 (0.27), residues: 1014 helix: 1.42 (0.56), residues: 103 sheet: -0.19 (0.27), residues: 372 loop : -1.06 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.025 0.001 PHE B 137 TYR 0.011 0.001 TYR A 275 ARG 0.002 0.000 ARG D 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: A 409 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8172 (ptp) outliers start: 23 outliers final: 19 residues processed: 95 average time/residue: 0.2156 time to fit residues: 28.9364 Evaluate side-chains 96 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094328 restraints weight = 14168.302| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.85 r_work: 0.3262 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8278 Z= 0.237 Angle : 0.617 10.322 11230 Z= 0.301 Chirality : 0.047 0.296 1292 Planarity : 0.004 0.044 1449 Dihedral : 8.759 84.368 1472 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.55 % Allowed : 19.83 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.74 (0.27), residues: 1014 helix: 1.38 (0.55), residues: 103 sheet: -0.19 (0.27), residues: 372 loop : -1.06 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.025 0.001 PHE B 137 TYR 0.010 0.001 TYR A 178 ARG 0.002 0.000 ARG A 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.15 seconds wall clock time: 38 minutes 5.23 seconds (2285.23 seconds total)