Starting phenix.real_space_refine on Sat Nov 16 01:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/11_2024/8oe4_16824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/11_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_16824/11_2024/8oe4_16824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/11_2024/8oe4_16824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/11_2024/8oe4_16824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe4_16824/11_2024/8oe4_16824.cif" } 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.51, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 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: 1.42 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: 3.89 Time building geometry restraints manager: 3.05 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: 0.00 - 3.31: 13767 3.31 - 6.62: 112 6.62 - 9.94: 10 9.94 - 13.25: 1 13.25 - 16.56: 2 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 3.040 nonbonded pdb=" O ASP A 84 " pdb=" OH TYR A 88 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 100 " pdb=" OG SER B 168 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 158 " pdb=" O GLU A 209 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU B 101 " pdb=" OG SER B 132 " model vdw 2.285 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.580 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.236 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: 0.2882 time to fit residues: 47.5533 Evaluate side-chains 63 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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: 20.0000 chunk 93 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0270 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS 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: 0.7632 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10205 Z= 0.207 Angle : 0.642 9.970 13892 Z= 0.326 Chirality : 0.045 0.160 1542 Planarity : 0.004 0.060 1777 Dihedral : 7.349 69.959 1513 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.56 % Allowed : 15.77 % Favored : 82.68 % 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 (0.23), residues: 1231 helix: 0.66 (0.51), residues: 105 sheet: 0.36 (0.21), residues: 515 loop : -0.53 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 371 HIS 0.006 0.001 HIS D 438 PHE 0.025 0.001 PHE C 75 TYR 0.019 0.001 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 89 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.686 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: 0.8520 (tpp) cc_final: 0.8228 (tpp) REVERT: A 270 SER cc_start: 0.9484 (m) cc_final: 0.8895 (p) REVERT: B 39 LYS cc_start: 0.8636 (tttp) cc_final: 0.8269 (mtmm) REVERT: B 107 ASP cc_start: 0.9011 (p0) cc_final: 0.8543 (t0) REVERT: C 99 MET cc_start: 0.8443 (mmm) cc_final: 0.7657 (mmt) REVERT: C 184 ASP cc_start: 0.9280 (m-30) cc_final: 0.8721 (t0) REVERT: D 136 SER cc_start: 0.8271 (m) cc_final: 0.7925 (t) REVERT: D 143 LEU cc_start: 0.8399 (mt) cc_final: 0.8039 (pp) REVERT: D 256 LEU cc_start: 0.9015 (tp) cc_final: 0.8782 (tt) REVERT: D 408 MET cc_start: 0.6325 (mtt) cc_final: 0.3888 (ttp) outliers start: 17 outliers final: 10 residues processed: 87 average time/residue: 0.2364 time to fit residues: 29.3253 Evaluate side-chains 66 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain D residue 93 SER 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: 6.9990 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 0.0030 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 75 HIS ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7756 moved from start: 0.2754 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= 0.461 Angle : 0.753 11.329 13892 Z= 0.382 Chirality : 0.048 0.183 1542 Planarity : 0.005 0.064 1777 Dihedral : 7.068 58.168 1510 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.76 % Allowed : 15.77 % Favored : 80.48 % 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: -0.19 (0.24), residues: 1231 helix: 0.73 (0.50), residues: 104 sheet: 0.31 (0.21), residues: 534 loop : -0.62 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 45 HIS 0.011 0.002 HIS A 216 PHE 0.015 0.002 PHE D 99 TYR 0.023 0.002 TYR D 36 ARG 0.006 0.001 ARG C 74 *********************** 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 99 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8469 (tpp) cc_final: 0.8129 (tpp) REVERT: A 250 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7952 (ttt90) REVERT: A 270 SER cc_start: 0.9493 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 298 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7781 (p) REVERT: B 39 LYS cc_start: 0.8669 (tttp) cc_final: 0.8313 (mtmm) REVERT: B 107 ASP cc_start: 0.9094 (p0) cc_final: 0.8645 (t0) REVERT: C 34 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (pt) REVERT: C 65 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: C 99 MET cc_start: 0.8709 (mmm) cc_final: 0.7739 (mmt) REVERT: C 184 ASP cc_start: 0.9261 (m-30) cc_final: 0.8754 (t0) REVERT: D 136 SER cc_start: 0.8437 (m) cc_final: 0.8157 (t) REVERT: D 256 LEU cc_start: 0.8923 (tp) cc_final: 0.8446 (pp) REVERT: D 408 MET cc_start: 0.6216 (mtt) cc_final: 0.3681 (tmm) outliers start: 41 outliers final: 24 residues processed: 95 average time/residue: 0.2173 time to fit residues: 30.1100 Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 298 VAL 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 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 D residue 93 SER Chi-restraints excluded: chain D residue 115 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: 6.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS D 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10205 Z= 0.303 Angle : 0.639 9.449 13892 Z= 0.324 Chirality : 0.044 0.169 1542 Planarity : 0.005 0.052 1777 Dihedral : 5.998 59.071 1510 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.02 % Allowed : 16.87 % 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: -0.19 (0.24), residues: 1231 helix: 0.95 (0.51), residues: 104 sheet: 0.18 (0.22), residues: 538 loop : -0.53 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.011 0.002 PHE A 140 TYR 0.018 0.002 TYR D 357 ARG 0.005 0.001 ARG C 74 *********************** 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 85 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8449 (tpp) cc_final: 0.8174 (tpp) REVERT: A 209 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: A 270 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.8921 (p) REVERT: B 39 LYS cc_start: 0.8696 (tttp) cc_final: 0.8354 (mtmm) REVERT: B 107 ASP cc_start: 0.8982 (p0) cc_final: 0.8481 (t0) REVERT: C 34 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8187 (pt) REVERT: C 44 MET cc_start: 0.8281 (mmm) cc_final: 0.7887 (mmm) REVERT: C 65 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6890 (t-90) REVERT: C 99 MET cc_start: 0.8665 (mmm) cc_final: 0.7730 (mmt) REVERT: C 142 MET cc_start: 0.9026 (mpp) cc_final: 0.8565 (mpp) REVERT: C 184 ASP cc_start: 0.9285 (m-30) cc_final: 0.8766 (t0) REVERT: D 136 SER cc_start: 0.8434 (m) cc_final: 0.8128 (t) REVERT: D 256 LEU cc_start: 0.8921 (tp) cc_final: 0.8421 (pp) REVERT: D 356 MET cc_start: 0.7911 (mtm) cc_final: 0.7565 (mpp) REVERT: D 408 MET cc_start: 0.6026 (mtt) cc_final: 0.3155 (tmm) REVERT: D 419 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8634 (m-80) outliers start: 33 outliers final: 22 residues processed: 80 average time/residue: 0.2169 time to fit residues: 25.5015 Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 209 GLU 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 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 154 ILE Chi-restraints excluded: chain C residue 161 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10205 Z= 0.197 Angle : 0.572 9.019 13892 Z= 0.289 Chirality : 0.043 0.211 1542 Planarity : 0.004 0.066 1777 Dihedral : 5.485 58.573 1510 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.02 % Allowed : 17.60 % Favored : 79.38 % 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: -0.06 (0.24), residues: 1231 helix: 1.18 (0.52), residues: 104 sheet: 0.27 (0.22), residues: 523 loop : -0.46 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.012 0.001 PHE A 140 TYR 0.018 0.001 TYR D 357 ARG 0.006 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 85 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8397 (tpp) cc_final: 0.8087 (tpp) REVERT: A 209 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: A 270 SER cc_start: 0.9543 (m) cc_final: 0.8978 (p) REVERT: A 298 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7848 (p) REVERT: B 39 LYS cc_start: 0.8715 (tttp) cc_final: 0.8368 (mtmm) REVERT: B 107 ASP cc_start: 0.8888 (p0) cc_final: 0.8422 (t0) REVERT: C 34 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8080 (pt) REVERT: C 65 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.6990 (t-90) REVERT: C 99 MET cc_start: 0.8648 (mmm) cc_final: 0.7778 (mmt) REVERT: C 142 MET cc_start: 0.8990 (mpp) cc_final: 0.8697 (mpp) REVERT: C 184 ASP cc_start: 0.9301 (m-30) cc_final: 0.8802 (t0) REVERT: D 136 SER cc_start: 0.8369 (m) cc_final: 0.8102 (t) REVERT: D 356 MET cc_start: 0.7916 (mtm) cc_final: 0.7448 (pmm) REVERT: D 408 MET cc_start: 0.6171 (mtt) cc_final: 0.2830 (tmm) REVERT: D 419 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8668 (m-80) outliers start: 33 outliers final: 22 residues processed: 81 average time/residue: 0.2060 time to fit residues: 25.2708 Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 209 GLU 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 298 VAL 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 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 93 SER Chi-restraints excluded: chain D residue 257 THR 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: 7.9990 chunk 23 optimal weight: 0.0570 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 0.2980 chunk 99 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.0678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10205 Z= 0.173 Angle : 0.568 9.391 13892 Z= 0.284 Chirality : 0.042 0.149 1542 Planarity : 0.004 0.069 1777 Dihedral : 5.261 57.375 1510 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 18.06 % Favored : 78.83 % 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: 0.02 (0.24), residues: 1231 helix: 1.13 (0.53), residues: 109 sheet: 0.32 (0.22), residues: 522 loop : -0.39 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 466 HIS 0.003 0.001 HIS C 65 PHE 0.012 0.001 PHE A 140 TYR 0.018 0.001 TYR D 357 ARG 0.008 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 to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8354 (tpp) cc_final: 0.8021 (tpp) REVERT: A 209 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: A 270 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 298 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 39 LYS cc_start: 0.8712 (tttp) cc_final: 0.8407 (mtmm) REVERT: C 65 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6855 (t-90) REVERT: C 99 MET cc_start: 0.8635 (mmm) cc_final: 0.7723 (mmt) REVERT: C 142 MET cc_start: 0.8977 (mpp) cc_final: 0.8571 (mpp) REVERT: C 204 MET cc_start: 0.7768 (tpp) cc_final: 0.7290 (tpp) REVERT: D 136 SER cc_start: 0.8357 (m) cc_final: 0.8100 (t) REVERT: D 408 MET cc_start: 0.6179 (mtt) cc_final: 0.3054 (tmm) outliers start: 34 outliers final: 23 residues processed: 80 average time/residue: 0.1990 time to fit residues: 24.1217 Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 209 GLU 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 298 VAL 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 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 93 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 309 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10205 Z= 0.279 Angle : 0.619 11.228 13892 Z= 0.312 Chirality : 0.043 0.151 1542 Planarity : 0.005 0.067 1777 Dihedral : 5.579 59.604 1510 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.02 % Allowed : 19.07 % Favored : 77.91 % 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: -0.01 (0.24), residues: 1231 helix: 1.31 (0.53), residues: 103 sheet: 0.35 (0.23), residues: 509 loop : -0.48 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.010 0.002 PHE B 109 TYR 0.016 0.002 TYR D 36 ARG 0.005 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 83 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: A 45 MET cc_start: 0.8345 (tpp) cc_final: 0.8018 (tpp) REVERT: A 209 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: A 270 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 298 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7780 (p) REVERT: B 39 LYS cc_start: 0.8736 (tttp) cc_final: 0.8426 (mtmm) REVERT: B 107 ASP cc_start: 0.9080 (p0) cc_final: 0.8621 (t0) REVERT: C 44 MET cc_start: 0.7864 (mmm) cc_final: 0.7392 (mmm) REVERT: C 65 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: C 99 MET cc_start: 0.8613 (mmm) cc_final: 0.7683 (mmt) REVERT: C 142 MET cc_start: 0.9119 (mpp) cc_final: 0.8731 (mpp) REVERT: C 204 MET cc_start: 0.7895 (tpp) cc_final: 0.7527 (tpp) REVERT: D 136 SER cc_start: 0.8421 (m) cc_final: 0.8162 (t) REVERT: D 408 MET cc_start: 0.6268 (mtt) cc_final: 0.2830 (tmm) outliers start: 33 outliers final: 25 residues processed: 78 average time/residue: 0.1950 time to fit residues: 23.0985 Evaluate side-chains 78 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 141 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 209 GLU 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 298 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 108 optimal weight: 30.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10205 Z= 0.246 Angle : 0.601 12.646 13892 Z= 0.299 Chirality : 0.042 0.154 1542 Planarity : 0.004 0.070 1777 Dihedral : 5.455 59.207 1510 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.39 % Allowed : 19.07 % Favored : 77.54 % 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: 0.01 (0.24), residues: 1231 helix: 1.55 (0.53), residues: 101 sheet: 0.27 (0.22), residues: 529 loop : -0.42 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 466 HIS 0.004 0.001 HIS C 65 PHE 0.011 0.001 PHE B 109 TYR 0.015 0.001 TYR D 36 ARG 0.007 0.000 ARG C 74 *********************** 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 85 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 48 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 45 MET cc_start: 0.8358 (tpp) cc_final: 0.8032 (tpp) REVERT: A 209 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: A 270 SER cc_start: 0.9487 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 298 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7768 (p) REVERT: B 39 LYS cc_start: 0.8731 (tttp) cc_final: 0.8432 (mtmm) REVERT: B 107 ASP cc_start: 0.9067 (p0) cc_final: 0.8631 (t0) REVERT: C 44 MET cc_start: 0.7718 (mmm) cc_final: 0.7347 (mmm) REVERT: C 65 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.6902 (t-90) REVERT: C 99 MET cc_start: 0.8607 (mmm) cc_final: 0.7691 (mmt) REVERT: C 142 MET cc_start: 0.9074 (mpp) cc_final: 0.8656 (mpp) REVERT: C 204 MET cc_start: 0.7920 (tpp) cc_final: 0.7648 (tpp) REVERT: D 136 SER cc_start: 0.8411 (m) cc_final: 0.8156 (t) REVERT: D 408 MET cc_start: 0.6339 (mtt) cc_final: 0.3099 (tmm) outliers start: 37 outliers final: 28 residues processed: 80 average time/residue: 0.2039 time to fit residues: 24.2559 Evaluate side-chains 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 141 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 209 GLU 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 298 VAL 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 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 Chi-restraints excluded: chain D residue 535 GLN 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: 9.9990 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 10205 Z= 0.492 Angle : 0.758 12.669 13892 Z= 0.382 Chirality : 0.047 0.167 1542 Planarity : 0.005 0.067 1777 Dihedral : 6.331 57.690 1510 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.30 % Allowed : 19.25 % Favored : 77.45 % 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: -0.50 (0.24), residues: 1231 helix: 0.49 (0.51), residues: 101 sheet: -0.06 (0.22), residues: 542 loop : -0.64 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 45 HIS 0.007 0.001 HIS C 65 PHE 0.017 0.003 PHE B 109 TYR 0.022 0.002 TYR D 36 ARG 0.010 0.001 ARG C 74 *********************** 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 85 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: A 120 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: A 192 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: A 270 SER cc_start: 0.9431 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 298 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7736 (p) REVERT: B 39 LYS cc_start: 0.8739 (tttp) cc_final: 0.8388 (mtmm) REVERT: C 99 MET cc_start: 0.8661 (mmm) cc_final: 0.7717 (mmt) REVERT: C 184 ASP cc_start: 0.9368 (m-30) cc_final: 0.8895 (t0) REVERT: D 136 SER cc_start: 0.8576 (m) cc_final: 0.8154 (p) REVERT: D 356 MET cc_start: 0.7779 (mtm) cc_final: 0.7380 (mpp) REVERT: D 408 MET cc_start: 0.6442 (mtt) cc_final: 0.3516 (tmm) outliers start: 36 outliers final: 26 residues processed: 79 average time/residue: 0.2155 time to fit residues: 25.2883 Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 141 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 192 GLU 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 298 VAL 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 77 ILE Chi-restraints excluded: chain C residue 78 THR 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 309 LEU Chi-restraints excluded: chain D residue 419 PHE 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: 5.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10205 Z= 0.281 Angle : 0.661 11.646 13892 Z= 0.329 Chirality : 0.044 0.217 1542 Planarity : 0.005 0.070 1777 Dihedral : 5.880 58.164 1510 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.12 % Allowed : 19.80 % 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: -0.34 (0.24), residues: 1231 helix: 1.04 (0.52), residues: 101 sheet: 0.02 (0.22), residues: 532 loop : -0.60 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 466 HIS 0.004 0.001 HIS C 313 PHE 0.010 0.002 PHE C 274 TYR 0.021 0.002 TYR D 36 ARG 0.010 0.001 ARG C 74 ********************** 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 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: A 120 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: A 192 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 270 SER cc_start: 0.9463 (OUTLIER) cc_final: 0.8815 (p) REVERT: A 298 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7787 (p) REVERT: B 39 LYS cc_start: 0.8740 (tttp) cc_final: 0.8385 (mtmm) REVERT: C 99 MET cc_start: 0.8599 (mmm) cc_final: 0.7662 (mmt) REVERT: C 142 MET cc_start: 0.9169 (mpp) cc_final: 0.8570 (mpp) REVERT: C 184 ASP cc_start: 0.9332 (m-30) cc_final: 0.8844 (t0) REVERT: D 136 SER cc_start: 0.8444 (m) cc_final: 0.8197 (t) REVERT: D 356 MET cc_start: 0.7822 (mtm) cc_final: 0.7459 (mpp) REVERT: D 408 MET cc_start: 0.6301 (mtt) cc_final: 0.3569 (tmm) outliers start: 34 outliers final: 26 residues processed: 76 average time/residue: 0.2001 time to fit residues: 23.2269 Evaluate side-chains 77 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 141 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 176 SER Chi-restraints excluded: chain A residue 192 GLU 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 298 VAL 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 41 ILE Chi-restraints excluded: chain C residue 78 THR 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 309 LEU Chi-restraints excluded: chain D residue 419 PHE 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 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 = 0.4194 r_free = 0.4194 target = 0.101161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067718 restraints weight = 48558.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066925 restraints weight = 28114.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067071 restraints weight = 17685.442| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10205 Z= 0.212 Angle : 0.624 12.838 13892 Z= 0.308 Chirality : 0.043 0.199 1542 Planarity : 0.004 0.069 1777 Dihedral : 5.545 56.022 1510 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 19.89 % Favored : 77.27 % 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: -0.10 (0.24), residues: 1231 helix: 1.49 (0.52), residues: 101 sheet: 0.15 (0.22), residues: 522 loop : -0.44 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 466 HIS 0.003 0.001 HIS C 65 PHE 0.010 0.001 PHE A 140 TYR 0.019 0.001 TYR D 36 ARG 0.010 0.001 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.29 seconds wall clock time: 36 minutes 34.41 seconds (2194.41 seconds total)