Starting phenix.real_space_refine on Thu Sep 18 01:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnz_45767/09_2025/9cnz_45767.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 8110 2.51 5 N 2212 2.21 5 O 2494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12854 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6207 Classifications: {'peptide': 785} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 754} Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2594 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 2 Chain: "C" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1181 Classifications: {'peptide': 158} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 10, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1755 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "G" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY G 0 " pdbres="PHE G 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY H 0 " pdbres="PHE H 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY I 0 " pdbres="PHE I 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.56, per 1000 atoms: 0.28 Number of scatterers: 12854 At special positions: 0 Unit cell: (117.835, 117.835, 141.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2494 8.00 N 2212 7.00 C 8110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 641.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2986 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 21 sheets defined 25.9% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 4.121A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.894A pdb=" N VAL A 208 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.733A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.895A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.578A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.554A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 4.171A pdb=" N TYR C 65 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.530A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 4.079A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 211 removed outlier: 3.788A pdb=" N LYS C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.729A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.519A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.586A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.072A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.617A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'G' and resid 5 through 9 removed outlier: 4.187A pdb=" N PHE G 9 " --> pdb=" O LYS G 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 8 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.912A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 100 removed outlier: 7.039A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.373A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.346A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.960A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.892A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.512A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 433 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 426 " --> pdb=" O PHE H 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.351A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.938A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.670A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.732A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.340A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.578A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.636A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.549A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.759A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.143A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.491A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.500A pdb=" N GLN C 172 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.064A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC3, first strand: chain 'I' and resid 2 through 4 599 hydrogen bonds defined for protein. 1635 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: 2.44 Time building geometry restraints manager: 1.41 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: 4257 1.34 - 1.46: 2345 1.46 - 1.57: 6454 1.57 - 1.69: 1 1.69 - 1.81: 71 Bond restraints: 13128 Sorted by residual: bond pdb=" CB PRO D 32 " pdb=" CG PRO D 32 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.25e+00 bond pdb=" CG PRO D 32 " pdb=" CD PRO D 32 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.57e+00 bond pdb=" C ACY G 0 " pdb=" O ACY G 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C ACY H 0 " pdb=" O ACY H 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" C ACY I 0 " pdb=" O ACY I 0 " ideal model delta sigma weight residual 1.248 1.283 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 13123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17442 2.00 - 3.99: 310 3.99 - 5.99: 53 5.99 - 7.98: 11 7.98 - 9.98: 2 Bond angle restraints: 17818 Sorted by residual: angle pdb=" CA PRO D 32 " pdb=" N PRO D 32 " pdb=" CD PRO D 32 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" N PRO D 32 " pdb=" CD PRO D 32 " pdb=" CG PRO D 32 " ideal model delta sigma weight residual 103.20 96.38 6.82 1.50e+00 4.44e-01 2.07e+01 angle pdb=" CA GLN D 44 " pdb=" CB GLN D 44 " pdb=" CG GLN D 44 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N ASN A 297 " pdb=" CA ASN A 297 " pdb=" C ASN A 297 " ideal model delta sigma weight residual 107.93 115.34 -7.41 1.65e+00 3.67e-01 2.01e+01 angle pdb=" C VAL B 254 " pdb=" N ASN B 255 " pdb=" CA ASN B 255 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 ... (remaining 17813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7087 17.85 - 35.69: 533 35.69 - 53.54: 77 53.54 - 71.38: 26 71.38 - 89.23: 18 Dihedral angle restraints: 7741 sinusoidal: 3043 harmonic: 4698 Sorted by residual: dihedral pdb=" CA ARG G 7 " pdb=" C ARG G 7 " pdb=" N ARG G 8 " pdb=" CA ARG G 8 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU A 689 " pdb=" C GLU A 689 " pdb=" N CYS A 690 " pdb=" CA CYS A 690 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR G 11 " pdb=" C TYR G 11 " pdb=" N TRP G 12 " pdb=" CA TRP G 12 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1579 0.059 - 0.118: 313 0.118 - 0.177: 37 0.177 - 0.236: 2 0.236 - 0.295: 2 Chirality restraints: 1933 Sorted by residual: chirality pdb=" CB THR B 43 " pdb=" CA THR B 43 " pdb=" OG1 THR B 43 " pdb=" CG2 THR B 43 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA TRP A 546 " pdb=" N TRP A 546 " pdb=" C TRP A 546 " pdb=" CB TRP A 546 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASN A 297 " pdb=" N ASN A 297 " pdb=" C ASN A 297 " pdb=" CB ASN A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1930 not shown) Planarity restraints: 2341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " 0.052 2.00e-02 2.50e+03 5.09e-02 6.48e+01 pdb=" CG TRP A 546 " -0.133 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 31 " -0.096 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO D 32 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 34 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" CD GLN E 34 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN E 34 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN E 34 " -0.015 2.00e-02 2.50e+03 ... (remaining 2338 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2865 2.79 - 3.32: 11601 3.32 - 3.84: 21178 3.84 - 4.37: 24537 4.37 - 4.90: 43463 Nonbonded interactions: 103644 Sorted by model distance: nonbonded pdb=" OH TYR A 468 " pdb=" OE1 GLU A 470 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP D 93 " pdb=" NH1 ARG D 112 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG C 112 " pdb=" OG1 THR C 115 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR B 73 " pdb=" OG1 THR B 136 " model vdw 2.296 3.040 nonbonded pdb=" O THR C 115 " pdb=" NE2 GLN C 119 " model vdw 2.301 3.120 ... (remaining 103639 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.004 0.135 13138 Z= 0.232 Angle : 0.680 9.978 17820 Z= 0.370 Chirality : 0.048 0.295 1933 Planarity : 0.006 0.138 2341 Dihedral : 13.574 89.228 4752 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.20), residues: 1616 helix: 1.09 (0.26), residues: 357 sheet: 0.42 (0.23), residues: 468 loop : -0.07 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 8 TYR 0.028 0.002 TYR D 62 PHE 0.029 0.002 PHE A 426 TRP 0.133 0.003 TRP A 546 HIS 0.005 0.001 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00395 (13128) covalent geometry : angle 0.68010 (17818) SS BOND : bond 0.00565 ( 1) SS BOND : angle 1.22569 ( 2) hydrogen bonds : bond 0.16265 ( 591) hydrogen bonds : angle 7.50216 ( 1635) Misc. bond : bond 0.05845 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0979 (tpt) cc_final: 0.0476 (tpp) REVERT: A 304 MET cc_start: 0.8215 (mtp) cc_final: 0.7925 (mtp) REVERT: A 325 MET cc_start: 0.7766 (tpt) cc_final: 0.7453 (tmm) REVERT: A 532 VAL cc_start: 0.9097 (p) cc_final: 0.8843 (t) REVERT: C 65 TYR cc_start: 0.8936 (m-80) cc_final: 0.8456 (m-80) REVERT: D 183 GLU cc_start: 0.7569 (tt0) cc_final: 0.7296 (mt-10) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1179 time to fit residues: 41.5106 Evaluate side-chains 207 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 350 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.162798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103730 restraints weight = 16838.103| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.11 r_work: 0.2867 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13138 Z= 0.182 Angle : 0.559 7.223 17820 Z= 0.302 Chirality : 0.045 0.169 1933 Planarity : 0.004 0.062 2341 Dihedral : 4.619 17.700 1798 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.66 % Allowed : 7.88 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1616 helix: 1.56 (0.27), residues: 360 sheet: 0.23 (0.22), residues: 483 loop : 0.05 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.023 0.002 TYR A 214 PHE 0.019 0.001 PHE D 127 TRP 0.036 0.002 TRP A 546 HIS 0.007 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00407 (13128) covalent geometry : angle 0.55818 (17818) SS BOND : bond 0.00525 ( 1) SS BOND : angle 3.11838 ( 2) hydrogen bonds : bond 0.04229 ( 591) hydrogen bonds : angle 5.60360 ( 1635) Misc. bond : bond 0.00063 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ARG cc_start: 0.7676 (ptm160) cc_final: 0.7440 (ptm160) REVERT: A 215 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 286 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8285 (tp40) REVERT: A 289 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8648 (ttmm) REVERT: A 304 MET cc_start: 0.8539 (mtp) cc_final: 0.8288 (mtp) REVERT: A 325 MET cc_start: 0.8379 (tpt) cc_final: 0.7675 (ppp) REVERT: A 422 ASN cc_start: 0.8733 (t0) cc_final: 0.8443 (t0) REVERT: A 728 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8035 (tmmt) REVERT: A 768 MET cc_start: 0.9095 (mtt) cc_final: 0.8891 (mtt) REVERT: B 361 LYS cc_start: 0.9035 (tppp) cc_final: 0.8537 (tppp) REVERT: C 202 MET cc_start: 0.8648 (ppp) cc_final: 0.8312 (ttt) REVERT: D 52 ILE cc_start: 0.9257 (mt) cc_final: 0.8941 (tp) REVERT: D 154 TYR cc_start: 0.8249 (m-80) cc_final: 0.7951 (m-80) REVERT: D 183 GLU cc_start: 0.8636 (tt0) cc_final: 0.8293 (mt-10) REVERT: E 25 ARG cc_start: 0.6799 (mmp80) cc_final: 0.6494 (mmp80) REVERT: I 7 ARG cc_start: 0.8847 (mpt-90) cc_final: 0.8239 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 219 average time/residue: 0.1165 time to fit residues: 36.5583 Evaluate side-chains 208 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 99 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 53 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106417 restraints weight = 16941.470| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.29 r_work: 0.2893 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13138 Z= 0.115 Angle : 0.499 7.005 17820 Z= 0.268 Chirality : 0.043 0.145 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.301 16.473 1798 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.88 % Allowed : 9.64 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1616 helix: 1.81 (0.27), residues: 361 sheet: 0.27 (0.22), residues: 490 loop : 0.13 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 8 TYR 0.019 0.001 TYR A 214 PHE 0.016 0.001 PHE A 428 TRP 0.015 0.001 TRP A 546 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00250 (13128) covalent geometry : angle 0.49907 (17818) SS BOND : bond 0.00432 ( 1) SS BOND : angle 1.78936 ( 2) hydrogen bonds : bond 0.03529 ( 591) hydrogen bonds : angle 5.06956 ( 1635) Misc. bond : bond 0.00031 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0594 (mmt) cc_final: 0.0306 (tpt) REVERT: A 215 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 286 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8235 (tp40) REVERT: A 289 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8631 (ttmm) REVERT: A 325 MET cc_start: 0.8332 (tpt) cc_final: 0.7713 (ppp) REVERT: A 422 ASN cc_start: 0.8768 (t0) cc_final: 0.8377 (t0) REVERT: A 438 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8643 (t) REVERT: A 440 PHE cc_start: 0.8034 (m-80) cc_final: 0.7411 (t80) REVERT: A 634 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8052 (ttt90) REVERT: A 700 CYS cc_start: 0.8098 (m) cc_final: 0.7826 (m) REVERT: B 84 LEU cc_start: 0.8286 (mt) cc_final: 0.8038 (mt) REVERT: C 202 MET cc_start: 0.8746 (ppp) cc_final: 0.8282 (ttt) REVERT: D 109 MET cc_start: 0.8164 (mtp) cc_final: 0.7944 (mtp) REVERT: D 154 TYR cc_start: 0.8272 (m-80) cc_final: 0.7953 (m-80) REVERT: E 25 ARG cc_start: 0.6918 (mmp80) cc_final: 0.6514 (mmp80) outliers start: 12 outliers final: 10 residues processed: 225 average time/residue: 0.1224 time to fit residues: 39.2635 Evaluate side-chains 212 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108705 restraints weight = 16930.051| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.39 r_work: 0.2870 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13138 Z= 0.136 Angle : 0.493 6.887 17820 Z= 0.264 Chirality : 0.043 0.138 1933 Planarity : 0.004 0.048 2341 Dihedral : 4.234 16.312 1798 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.61 % Allowed : 10.58 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1616 helix: 1.90 (0.27), residues: 361 sheet: 0.28 (0.22), residues: 494 loop : 0.16 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 8 TYR 0.020 0.001 TYR A 296 PHE 0.019 0.001 PHE D 127 TRP 0.010 0.001 TRP A 745 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00302 (13128) covalent geometry : angle 0.49295 (17818) SS BOND : bond 0.00440 ( 1) SS BOND : angle 1.66703 ( 2) hydrogen bonds : bond 0.03462 ( 591) hydrogen bonds : angle 4.91528 ( 1635) Misc. bond : bond 0.00041 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0532 (mmp) cc_final: -0.2137 (mtt) REVERT: A 215 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 286 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8237 (tp40) REVERT: A 289 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8596 (ttmm) REVERT: A 325 MET cc_start: 0.8332 (tpt) cc_final: 0.7745 (ppp) REVERT: A 422 ASN cc_start: 0.8778 (t0) cc_final: 0.8423 (t0) REVERT: A 438 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (t) REVERT: A 440 PHE cc_start: 0.8107 (m-80) cc_final: 0.7474 (t80) REVERT: A 536 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8597 (mt) REVERT: A 634 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8063 (ttt90) REVERT: A 700 CYS cc_start: 0.8070 (m) cc_final: 0.7771 (m) REVERT: B 43 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8902 (p) REVERT: C 202 MET cc_start: 0.8732 (ppp) cc_final: 0.8389 (tmm) REVERT: D 44 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7814 (pp30) REVERT: I 7 ARG cc_start: 0.8810 (mmt90) cc_final: 0.8106 (mmm-85) outliers start: 22 outliers final: 17 residues processed: 215 average time/residue: 0.1187 time to fit residues: 36.7949 Evaluate side-chains 218 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3883 r_free = 0.3883 target = 0.160772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107022 restraints weight = 17043.349| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.44 r_work: 0.2834 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13138 Z= 0.260 Angle : 0.558 6.585 17820 Z= 0.298 Chirality : 0.045 0.147 1933 Planarity : 0.004 0.050 2341 Dihedral : 4.476 19.762 1798 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.70 % Allowed : 10.95 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.21), residues: 1616 helix: 1.83 (0.27), residues: 361 sheet: 0.20 (0.22), residues: 500 loop : 0.06 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 8 TYR 0.017 0.002 TYR A 649 PHE 0.017 0.002 PHE A 428 TRP 0.012 0.002 TRP A 376 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00589 (13128) covalent geometry : angle 0.55778 (17818) SS BOND : bond 0.00643 ( 1) SS BOND : angle 2.24480 ( 2) hydrogen bonds : bond 0.04002 ( 591) hydrogen bonds : angle 5.14932 ( 1635) Misc. bond : bond 0.00077 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1123 (mmp) cc_final: -0.1555 (mtt) REVERT: A 189 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 215 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 286 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8270 (tp40) REVERT: A 289 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8595 (ttmm) REVERT: A 325 MET cc_start: 0.8342 (tpt) cc_final: 0.7742 (ppp) REVERT: A 422 ASN cc_start: 0.8870 (t0) cc_final: 0.8551 (t0) REVERT: A 440 PHE cc_start: 0.8154 (m-80) cc_final: 0.7453 (t80) REVERT: A 536 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8842 (mp) REVERT: B 43 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8916 (p) REVERT: C 202 MET cc_start: 0.8819 (ppp) cc_final: 0.8383 (tmm) REVERT: D 44 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7806 (pp30) REVERT: D 149 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8524 (mtmm) outliers start: 37 outliers final: 28 residues processed: 221 average time/residue: 0.1095 time to fit residues: 35.2901 Evaluate side-chains 225 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3904 r_free = 0.3904 target = 0.162582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104753 restraints weight = 16793.090| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.25 r_work: 0.2842 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13138 Z= 0.132 Angle : 0.500 6.985 17820 Z= 0.266 Chirality : 0.043 0.150 1933 Planarity : 0.004 0.049 2341 Dihedral : 4.242 16.459 1798 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.26 % Allowed : 11.75 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1616 helix: 1.98 (0.27), residues: 362 sheet: 0.24 (0.22), residues: 494 loop : 0.13 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 7 TYR 0.018 0.001 TYR D 184 PHE 0.017 0.001 PHE A 428 TRP 0.012 0.001 TRP A 745 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00292 (13128) covalent geometry : angle 0.50008 (17818) SS BOND : bond 0.00502 ( 1) SS BOND : angle 1.55526 ( 2) hydrogen bonds : bond 0.03416 ( 591) hydrogen bonds : angle 4.86137 ( 1635) Misc. bond : bond 0.00041 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1032 (mmp) cc_final: -0.1557 (mtt) REVERT: A 189 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 215 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 286 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8293 (tp40) REVERT: A 325 MET cc_start: 0.8315 (tpt) cc_final: 0.7703 (ppp) REVERT: A 422 ASN cc_start: 0.8870 (t0) cc_final: 0.8555 (t0) REVERT: A 438 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 440 PHE cc_start: 0.8163 (m-80) cc_final: 0.7418 (t80) REVERT: A 536 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 634 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8186 (ttt90) REVERT: B 43 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 202 MET cc_start: 0.8827 (ppp) cc_final: 0.8385 (tmm) REVERT: D 44 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7793 (pp30) REVERT: D 149 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8418 (mtmm) REVERT: D 183 GLU cc_start: 0.8651 (tt0) cc_final: 0.8302 (mt-10) REVERT: I 7 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8167 (mmm-85) outliers start: 31 outliers final: 21 residues processed: 221 average time/residue: 0.1164 time to fit residues: 37.1314 Evaluate side-chains 222 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 136 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3910 r_free = 0.3910 target = 0.163072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104210 restraints weight = 16838.433| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.10 r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13138 Z= 0.128 Angle : 0.492 6.896 17820 Z= 0.261 Chirality : 0.043 0.144 1933 Planarity : 0.004 0.049 2341 Dihedral : 4.124 15.993 1798 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.63 % Allowed : 12.19 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.21), residues: 1616 helix: 2.04 (0.27), residues: 362 sheet: 0.24 (0.22), residues: 496 loop : 0.20 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 25 TYR 0.018 0.001 TYR D 62 PHE 0.016 0.001 PHE A 428 TRP 0.011 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00283 (13128) covalent geometry : angle 0.49214 (17818) SS BOND : bond 0.00367 ( 1) SS BOND : angle 1.33828 ( 2) hydrogen bonds : bond 0.03305 ( 591) hydrogen bonds : angle 4.72370 ( 1635) Misc. bond : bond 0.00037 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1154 (mmp) cc_final: -0.1501 (mtt) REVERT: A 189 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (p) REVERT: A 286 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8310 (tp40) REVERT: A 325 MET cc_start: 0.8280 (tpt) cc_final: 0.7797 (ppp) REVERT: A 338 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: A 422 ASN cc_start: 0.8758 (t0) cc_final: 0.8473 (t0) REVERT: A 438 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8716 (t) REVERT: A 440 PHE cc_start: 0.8135 (m-80) cc_final: 0.7542 (t80) REVERT: A 536 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 574 TYR cc_start: 0.8969 (p90) cc_final: 0.8751 (p90) REVERT: A 634 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8177 (ttt90) REVERT: B 43 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8869 (p) REVERT: D 44 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7785 (pp30) REVERT: D 112 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: E 88 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: I 7 ARG cc_start: 0.8732 (mmt90) cc_final: 0.8199 (mmm-85) outliers start: 36 outliers final: 29 residues processed: 227 average time/residue: 0.1145 time to fit residues: 38.0627 Evaluate side-chains 233 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108532 restraints weight = 16792.091| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.53 r_work: 0.2865 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13138 Z= 0.122 Angle : 0.490 6.871 17820 Z= 0.259 Chirality : 0.043 0.137 1933 Planarity : 0.003 0.050 2341 Dihedral : 4.050 15.723 1798 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 12.85 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1616 helix: 2.14 (0.27), residues: 362 sheet: 0.33 (0.22), residues: 490 loop : 0.19 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 25 TYR 0.022 0.001 TYR A 296 PHE 0.017 0.001 PHE A 428 TRP 0.011 0.001 TRP A 745 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00270 (13128) covalent geometry : angle 0.48969 (17818) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.27955 ( 2) hydrogen bonds : bond 0.03230 ( 591) hydrogen bonds : angle 4.64705 ( 1635) Misc. bond : bond 0.00036 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1182 (mmp) cc_final: -0.1449 (mtt) REVERT: A 189 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 286 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8381 (tp40) REVERT: A 325 MET cc_start: 0.8356 (tpt) cc_final: 0.7758 (ppp) REVERT: A 422 ASN cc_start: 0.8897 (t0) cc_final: 0.8589 (t0) REVERT: A 438 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 440 PHE cc_start: 0.8136 (m-80) cc_final: 0.7411 (t80) REVERT: A 536 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8648 (mt) REVERT: A 574 TYR cc_start: 0.9067 (p90) cc_final: 0.8838 (p90) REVERT: A 634 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8102 (ttt90) REVERT: B 43 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8908 (p) REVERT: C 202 MET cc_start: 0.7965 (tmm) cc_final: 0.7076 (tmm) REVERT: D 44 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7757 (pp30) REVERT: D 79 TYR cc_start: 0.8616 (m-80) cc_final: 0.8398 (m-80) REVERT: D 112 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8100 (ptm160) REVERT: E 88 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.7049 (tp40) REVERT: I 7 ARG cc_start: 0.8742 (mmt90) cc_final: 0.8127 (mmm-85) outliers start: 34 outliers final: 28 residues processed: 227 average time/residue: 0.1141 time to fit residues: 37.8551 Evaluate side-chains 236 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3896 r_free = 0.3896 target = 0.161909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106803 restraints weight = 16991.325| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.56 r_work: 0.2813 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13138 Z= 0.200 Angle : 0.532 10.257 17820 Z= 0.280 Chirality : 0.044 0.143 1933 Planarity : 0.004 0.050 2341 Dihedral : 4.199 17.683 1798 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.70 % Allowed : 12.70 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1616 helix: 2.02 (0.27), residues: 362 sheet: 0.25 (0.22), residues: 505 loop : 0.18 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 8 TYR 0.019 0.002 TYR A 296 PHE 0.017 0.001 PHE A 428 TRP 0.012 0.001 TRP H 12 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00454 (13128) covalent geometry : angle 0.53148 (17818) SS BOND : bond 0.00378 ( 1) SS BOND : angle 1.65439 ( 2) hydrogen bonds : bond 0.03582 ( 591) hydrogen bonds : angle 4.84002 ( 1635) Misc. bond : bond 0.00062 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1477 (mmp) cc_final: -0.1026 (mtt) REVERT: A 189 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 286 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8325 (tp40) REVERT: A 325 MET cc_start: 0.8353 (tpt) cc_final: 0.7691 (ppp) REVERT: A 338 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: A 422 ASN cc_start: 0.8964 (t0) cc_final: 0.8666 (t0) REVERT: A 438 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 440 PHE cc_start: 0.8165 (m-80) cc_final: 0.7377 (t80) REVERT: A 536 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 574 TYR cc_start: 0.9098 (p90) cc_final: 0.8870 (p90) REVERT: B 361 LYS cc_start: 0.9070 (tppp) cc_final: 0.8601 (ttmm) REVERT: C 39 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8317 (mp0) REVERT: D 44 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7759 (pp30) REVERT: D 146 ASP cc_start: 0.8020 (m-30) cc_final: 0.7798 (m-30) REVERT: E 88 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.7071 (tp40) REVERT: I 7 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8133 (mmm-85) outliers start: 37 outliers final: 29 residues processed: 224 average time/residue: 0.1146 time to fit residues: 37.1436 Evaluate side-chains 232 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3913 r_free = 0.3913 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107892 restraints weight = 16841.745| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.46 r_work: 0.2863 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13138 Z= 0.121 Angle : 0.518 14.658 17820 Z= 0.269 Chirality : 0.043 0.138 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.056 16.179 1798 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.19 % Allowed : 13.28 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1616 helix: 2.10 (0.27), residues: 362 sheet: 0.31 (0.22), residues: 499 loop : 0.21 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 8 TYR 0.022 0.001 TYR A 296 PHE 0.016 0.001 PHE A 428 TRP 0.011 0.001 TRP A 745 HIS 0.002 0.000 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00267 (13128) covalent geometry : angle 0.51820 (17818) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.35508 ( 2) hydrogen bonds : bond 0.03265 ( 591) hydrogen bonds : angle 4.66002 ( 1635) Misc. bond : bond 0.00036 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1464 (mmp) cc_final: -0.1034 (mtt) REVERT: A 189 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 286 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8363 (tp40) REVERT: A 325 MET cc_start: 0.8301 (tpt) cc_final: 0.7671 (ppp) REVERT: A 338 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7795 (ttm-80) REVERT: A 422 ASN cc_start: 0.8925 (t0) cc_final: 0.8638 (t0) REVERT: A 438 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8633 (t) REVERT: A 440 PHE cc_start: 0.8114 (m-80) cc_final: 0.7388 (t80) REVERT: A 536 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 574 TYR cc_start: 0.9061 (p90) cc_final: 0.8848 (p90) REVERT: A 634 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8106 (ttt90) REVERT: B 361 LYS cc_start: 0.9050 (tppp) cc_final: 0.8601 (tppp) REVERT: D 44 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7820 (pp30) REVERT: D 79 TYR cc_start: 0.8552 (m-80) cc_final: 0.8267 (m-10) REVERT: D 112 ARG cc_start: 0.8250 (ptm160) cc_final: 0.7723 (tmm-80) REVERT: E 88 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.7042 (tp40) REVERT: I 7 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8090 (mmm-85) outliers start: 30 outliers final: 25 residues processed: 223 average time/residue: 0.1189 time to fit residues: 38.0665 Evaluate side-chains 232 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 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 = 0.3890 r_free = 0.3890 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105571 restraints weight = 16793.935| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.59 r_work: 0.2820 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13138 Z= 0.223 Angle : 0.550 13.496 17820 Z= 0.288 Chirality : 0.044 0.143 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.217 17.942 1798 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 13.43 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1616 helix: 2.03 (0.27), residues: 362 sheet: 0.32 (0.22), residues: 501 loop : 0.11 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 8 TYR 0.019 0.002 TYR A 296 PHE 0.017 0.002 PHE H 13 TRP 0.013 0.001 TRP H 12 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00507 (13128) covalent geometry : angle 0.54954 (17818) SS BOND : bond 0.00397 ( 1) SS BOND : angle 1.70376 ( 2) hydrogen bonds : bond 0.03674 ( 591) hydrogen bonds : angle 4.87769 ( 1635) Misc. bond : bond 0.00068 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4685.28 seconds wall clock time: 80 minutes 26.01 seconds (4826.01 seconds total)