Starting phenix.real_space_refine on Wed Jun 11 16:34:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnz_45767/06_2025/9cnz_45767.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnz_45767/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnz_45767/06_2025/9cnz_45767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnz_45767/06_2025/9cnz_45767.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnz_45767/06_2025/9cnz_45767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnz_45767/06_2025/9cnz_45767.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.19, per 1000 atoms: 0.64 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.46 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: 4.78 Time building geometry restraints manager: 3.69 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.133 0.003 TRP A 546 HIS 0.005 0.001 HIS I 5 PHE 0.029 0.002 PHE A 426 TYR 0.028 0.002 TYR D 62 ARG 0.010 0.001 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.16265 ( 591) hydrogen bonds : angle 7.50216 ( 1635) SS BOND : bond 0.00565 ( 1) SS BOND : angle 1.22569 ( 2) covalent geometry : bond 0.00395 (13128) covalent geometry : angle 0.68010 (17818) 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 : 1.318 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: 0.2685 time to fit residues: 94.1672 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 : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.7980 chunk 120 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109160 restraints weight = 16806.498| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.34 r_work: 0.2964 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13138 Z= 0.143 Angle : 0.536 6.968 17820 Z= 0.289 Chirality : 0.044 0.157 1933 Planarity : 0.004 0.061 2341 Dihedral : 4.536 17.577 1798 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.66 % Allowed : 7.74 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1616 helix: 1.62 (0.27), residues: 360 sheet: 0.23 (0.22), residues: 483 loop : 0.09 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 546 HIS 0.007 0.001 HIS D 102 PHE 0.020 0.001 PHE D 127 TYR 0.025 0.002 TYR A 214 ARG 0.005 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 591) hydrogen bonds : angle 5.43630 ( 1635) SS BOND : bond 0.00604 ( 1) SS BOND : angle 2.89747 ( 2) covalent geometry : bond 0.00315 (13128) covalent geometry : angle 0.53560 (17818) Misc. bond : bond 0.00039 ( 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 227 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 TYR cc_start: 0.8684 (t80) cc_final: 0.8419 (t80) REVERT: A 215 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 286 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8302 (tp40) REVERT: A 289 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8642 (ttmm) REVERT: A 304 MET cc_start: 0.8528 (mtp) cc_final: 0.8268 (mtp) REVERT: A 325 MET cc_start: 0.8378 (tpt) cc_final: 0.7780 (ppp) REVERT: A 338 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7631 (ttm-80) REVERT: A 440 PHE cc_start: 0.8123 (m-80) cc_final: 0.7424 (t80) REVERT: B 361 LYS cc_start: 0.9011 (tppp) cc_final: 0.8525 (tppp) REVERT: D 52 ILE cc_start: 0.9259 (mt) cc_final: 0.9011 (tp) REVERT: D 154 TYR cc_start: 0.8225 (m-80) cc_final: 0.8016 (m-80) REVERT: D 183 GLU cc_start: 0.8621 (tt0) cc_final: 0.8271 (mt-10) REVERT: E 25 ARG cc_start: 0.6598 (mmp80) cc_final: 0.6336 (mmp80) REVERT: I 7 ARG cc_start: 0.8828 (mpt-90) cc_final: 0.8246 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 223 average time/residue: 0.2753 time to fit residues: 87.8847 Evaluate side-chains 209 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 THR 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 115 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 114 optimal weight: 0.0040 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111960 restraints weight = 16856.419| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.41 r_work: 0.2956 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1441 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= 0.122 Angle : 0.500 6.958 17820 Z= 0.267 Chirality : 0.043 0.141 1933 Planarity : 0.004 0.047 2341 Dihedral : 4.290 16.423 1798 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1616 helix: 1.84 (0.27), residues: 361 sheet: 0.28 (0.22), residues: 490 loop : 0.13 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 546 HIS 0.005 0.001 HIS D 102 PHE 0.016 0.001 PHE A 428 TYR 0.018 0.001 TYR D 184 ARG 0.005 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 591) hydrogen bonds : angle 5.04585 ( 1635) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.61026 ( 2) covalent geometry : bond 0.00267 (13128) covalent geometry : angle 0.49976 (17818) Misc. bond : bond 0.00047 ( 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 231 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0582 (mmt) cc_final: -0.2105 (mtt) REVERT: A 215 GLN cc_start: 0.8008 (tm-30) cc_final: 0.6909 (tm-30) REVERT: A 286 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8225 (tp40) REVERT: A 289 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8618 (ttmm) REVERT: A 325 MET cc_start: 0.8338 (tpt) cc_final: 0.7736 (ppp) REVERT: A 338 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: A 422 ASN cc_start: 0.8737 (t0) cc_final: 0.8425 (t0) REVERT: A 438 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8659 (t) REVERT: A 440 PHE cc_start: 0.8072 (m-80) cc_final: 0.7391 (t80) REVERT: A 634 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8003 (ttt90) REVERT: A 700 CYS cc_start: 0.7939 (m) cc_final: 0.7635 (m) REVERT: B 84 LEU cc_start: 0.8277 (mt) cc_final: 0.8059 (mt) REVERT: C 202 MET cc_start: 0.8739 (ppp) cc_final: 0.8266 (ttt) REVERT: D 154 TYR cc_start: 0.8280 (m-80) cc_final: 0.7999 (m-80) REVERT: E 25 ARG cc_start: 0.6926 (mmp80) cc_final: 0.6534 (mmp80) outliers start: 12 outliers final: 10 residues processed: 223 average time/residue: 0.2667 time to fit residues: 85.7720 Evaluate side-chains 213 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 A residue 735 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 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 55 optimal weight: 0.2980 chunk 78 optimal weight: 0.0030 chunk 123 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110210 restraints weight = 16724.139| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.42 r_work: 0.2872 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1641 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= 0.141 Angle : 0.495 6.945 17820 Z= 0.264 Chirality : 0.043 0.137 1933 Planarity : 0.003 0.046 2341 Dihedral : 4.229 16.506 1798 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.75 % Allowed : 10.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1616 helix: 1.93 (0.27), residues: 361 sheet: 0.31 (0.22), residues: 494 loop : 0.17 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.004 0.001 HIS D 102 PHE 0.018 0.001 PHE D 127 TYR 0.020 0.001 TYR A 296 ARG 0.005 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 591) hydrogen bonds : angle 4.91537 ( 1635) SS BOND : bond 0.00435 ( 1) SS BOND : angle 1.55728 ( 2) covalent geometry : bond 0.00313 (13128) covalent geometry : angle 0.49443 (17818) Misc. bond : bond 0.00045 ( 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 231 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0525 (mmp) cc_final: -0.2143 (mtt) REVERT: A 215 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 286 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8244 (tp40) REVERT: A 289 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8600 (ttmm) REVERT: A 325 MET cc_start: 0.8328 (tpt) cc_final: 0.7718 (ppp) REVERT: A 338 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: A 422 ASN cc_start: 0.8757 (t0) cc_final: 0.8455 (t0) REVERT: A 438 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 440 PHE cc_start: 0.8104 (m-80) cc_final: 0.7411 (t80) REVERT: A 536 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8591 (mt) REVERT: A 634 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8075 (ttt90) REVERT: B 43 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8901 (p) REVERT: C 202 MET cc_start: 0.8757 (ppp) cc_final: 0.8401 (tmm) REVERT: D 44 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7806 (pp30) REVERT: D 149 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: D 154 TYR cc_start: 0.8336 (m-80) cc_final: 0.8070 (m-80) REVERT: I 7 ARG cc_start: 0.8779 (mmt90) cc_final: 0.8081 (mmm-85) outliers start: 24 outliers final: 17 residues processed: 219 average time/residue: 0.2565 time to fit residues: 81.8650 Evaluate side-chains 218 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 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 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 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 149 LYS Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL 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 99 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 98 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.161024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.101597 restraints weight = 16891.404| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.09 r_work: 0.2825 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13138 Z= 0.249 Angle : 0.553 6.676 17820 Z= 0.295 Chirality : 0.045 0.156 1933 Planarity : 0.004 0.048 2341 Dihedral : 4.451 19.515 1798 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.77 % Allowed : 10.80 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1616 helix: 1.85 (0.27), residues: 362 sheet: 0.24 (0.22), residues: 498 loop : 0.06 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 376 HIS 0.004 0.001 HIS D 139 PHE 0.019 0.002 PHE D 127 TYR 0.018 0.002 TYR A 649 ARG 0.005 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 591) hydrogen bonds : angle 5.12973 ( 1635) SS BOND : bond 0.00544 ( 1) SS BOND : angle 2.04596 ( 2) covalent geometry : bond 0.00565 (13128) covalent geometry : angle 0.55222 (17818) Misc. bond : bond 0.00075 ( 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 242 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0918 (mmp) cc_final: -0.1726 (mtt) REVERT: A 189 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 286 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8261 (tp40) REVERT: A 289 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8577 (ttmm) REVERT: A 325 MET cc_start: 0.8342 (tpt) cc_final: 0.7740 (ppp) REVERT: A 338 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: A 422 ASN cc_start: 0.8859 (t0) cc_final: 0.8612 (t0) REVERT: A 536 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8808 (mp) REVERT: B 43 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8924 (p) REVERT: C 202 MET cc_start: 0.8772 (ppp) cc_final: 0.8333 (tmm) REVERT: D 44 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7791 (pp30) REVERT: D 112 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8141 (tmm-80) REVERT: D 149 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8426 (mtmm) REVERT: I 7 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8073 (mmm-85) outliers start: 38 outliers final: 25 residues processed: 225 average time/residue: 0.3443 time to fit residues: 114.9585 Evaluate side-chains 224 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 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 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 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 E residue 86 VAL 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 45 optimal weight: 0.0980 chunk 54 optimal weight: 0.0270 chunk 119 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 132 optimal weight: 0.7980 overall best weight: 0.2438 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.164596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106036 restraints weight = 17100.853| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.11 r_work: 0.2927 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13138 Z= 0.091 Angle : 0.477 6.977 17820 Z= 0.253 Chirality : 0.042 0.145 1933 Planarity : 0.003 0.048 2341 Dihedral : 4.059 14.714 1798 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 12.19 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1616 helix: 2.12 (0.27), residues: 362 sheet: 0.31 (0.22), residues: 488 loop : 0.22 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 376 HIS 0.003 0.001 HIS B 324 PHE 0.017 0.001 PHE D 127 TYR 0.018 0.001 TYR D 184 ARG 0.006 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 591) hydrogen bonds : angle 4.62239 ( 1635) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.09153 ( 2) covalent geometry : bond 0.00191 (13128) covalent geometry : angle 0.47647 (17818) Misc. bond : bond 0.00031 ( 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 237 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0931 (mmp) cc_final: -0.1677 (mtt) REVERT: A 189 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 218 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7667 (mtmt) REVERT: A 286 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8383 (tp40) REVERT: A 325 MET cc_start: 0.8278 (tpt) cc_final: 0.7750 (ppp) REVERT: A 338 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: A 422 ASN cc_start: 0.8744 (t0) cc_final: 0.8506 (t0) REVERT: A 440 PHE cc_start: 0.8093 (m-80) cc_final: 0.7414 (t80) REVERT: A 536 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 634 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8100 (ttt90) REVERT: B 43 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8860 (p) REVERT: C 202 MET cc_start: 0.8805 (ppp) cc_final: 0.8330 (tmm) REVERT: D 44 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7761 (pp30) REVERT: D 79 TYR cc_start: 0.8609 (m-80) cc_final: 0.8334 (m-10) REVERT: I 7 ARG cc_start: 0.8732 (mmt90) cc_final: 0.8082 (mmm-85) outliers start: 24 outliers final: 18 residues processed: 228 average time/residue: 0.2493 time to fit residues: 82.1079 Evaluate side-chains 222 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 444 VAL 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 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 164 ILE 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 71 VAL 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 158 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 0 optimal weight: 80.0000 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 427 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.162586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107628 restraints weight = 16776.448| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.42 r_work: 0.2915 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13138 Z= 0.173 Angle : 0.506 6.789 17820 Z= 0.269 Chirality : 0.043 0.139 1933 Planarity : 0.004 0.049 2341 Dihedral : 4.143 16.673 1798 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.63 % Allowed : 12.04 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1616 helix: 2.07 (0.27), residues: 362 sheet: 0.30 (0.22), residues: 487 loop : 0.16 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.002 0.001 HIS D 102 PHE 0.015 0.001 PHE A 428 TYR 0.020 0.002 TYR A 296 ARG 0.007 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 591) hydrogen bonds : angle 4.77468 ( 1635) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.50198 ( 2) covalent geometry : bond 0.00389 (13128) covalent geometry : angle 0.50571 (17818) Misc. bond : bond 0.00053 ( 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 238 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1167 (mmp) cc_final: -0.1481 (mtt) REVERT: A 189 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 218 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7664 (mtmt) REVERT: A 286 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8356 (tp40) REVERT: A 325 MET cc_start: 0.8337 (tpt) cc_final: 0.7737 (ppp) REVERT: A 338 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: A 422 ASN cc_start: 0.8842 (t0) cc_final: 0.8601 (t0) REVERT: A 438 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8716 (t) REVERT: A 440 PHE cc_start: 0.8127 (m-80) cc_final: 0.7373 (t80) REVERT: A 536 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8772 (mp) REVERT: A 574 TYR cc_start: 0.9069 (p90) cc_final: 0.8830 (p90) REVERT: A 634 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8130 (ttt90) REVERT: B 43 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8914 (p) REVERT: C 202 MET cc_start: 0.8859 (ppp) cc_final: 0.8413 (tmm) REVERT: D 44 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7776 (pp30) REVERT: D 112 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8103 (tmm-80) REVERT: D 149 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: I 7 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8069 (mmm-85) outliers start: 36 outliers final: 29 residues processed: 223 average time/residue: 0.3533 time to fit residues: 115.1102 Evaluate side-chains 234 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 LYS 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 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 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 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 H residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106017 restraints weight = 16944.870| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.53 r_work: 0.2804 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13138 Z= 0.208 Angle : 0.532 11.290 17820 Z= 0.280 Chirality : 0.044 0.144 1933 Planarity : 0.004 0.050 2341 Dihedral : 4.244 17.901 1798 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.55 % Allowed : 12.41 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1616 helix: 2.05 (0.27), residues: 362 sheet: 0.28 (0.22), residues: 488 loop : 0.09 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 12 HIS 0.003 0.001 HIS D 139 PHE 0.016 0.001 PHE A 428 TYR 0.019 0.002 TYR A 296 ARG 0.007 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 591) hydrogen bonds : angle 4.88122 ( 1635) SS BOND : bond 0.00413 ( 1) SS BOND : angle 1.79050 ( 2) covalent geometry : bond 0.00470 (13128) covalent geometry : angle 0.53187 (17818) Misc. bond : bond 0.00061 ( 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 235 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1215 (mmp) cc_final: -0.1430 (mtt) REVERT: A 189 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 212 ARG cc_start: 0.8010 (ptt180) cc_final: 0.7687 (ptt180) REVERT: A 286 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8372 (tp40) REVERT: A 325 MET cc_start: 0.8345 (tpt) cc_final: 0.7689 (ppp) REVERT: A 338 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: A 422 ASN cc_start: 0.8928 (t0) cc_final: 0.8673 (t0) REVERT: A 438 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8686 (t) REVERT: A 536 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 574 TYR cc_start: 0.9095 (p90) cc_final: 0.8864 (p90) REVERT: B 360 GLN cc_start: 0.8646 (tt0) cc_final: 0.8442 (tt0) REVERT: B 361 LYS cc_start: 0.9104 (tppp) cc_final: 0.8652 (ttmm) REVERT: C 202 MET cc_start: 0.8876 (ppp) cc_final: 0.8430 (tmm) REVERT: D 44 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7777 (pp30) REVERT: E 88 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.7085 (tp40) REVERT: I 7 ARG cc_start: 0.8760 (mmt90) cc_final: 0.8032 (mmm-85) outliers start: 35 outliers final: 30 residues processed: 222 average time/residue: 0.2765 time to fit residues: 89.0070 Evaluate side-chains 232 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 LYS 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 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 315 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 125 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 301 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106550 restraints weight = 16797.241| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.57 r_work: 0.2822 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13138 Z= 0.162 Angle : 0.518 14.583 17820 Z= 0.271 Chirality : 0.043 0.140 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.150 16.651 1798 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.48 % Allowed : 12.48 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1616 helix: 2.02 (0.27), residues: 362 sheet: 0.27 (0.22), residues: 499 loop : 0.14 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 PHE 0.017 0.001 PHE A 428 TYR 0.019 0.002 TYR A 296 ARG 0.007 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 591) hydrogen bonds : angle 4.77786 ( 1635) SS BOND : bond 0.00386 ( 1) SS BOND : angle 1.50801 ( 2) covalent geometry : bond 0.00364 (13128) covalent geometry : angle 0.51734 (17818) Misc. bond : bond 0.00049 ( 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 236 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1489 (mmp) cc_final: -0.1019 (mtt) REVERT: A 189 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8122 (p) REVERT: A 212 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7716 (ptt180) REVERT: A 286 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8369 (tp40) REVERT: A 325 MET cc_start: 0.8344 (tpt) cc_final: 0.7710 (ppp) REVERT: A 338 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: A 422 ASN cc_start: 0.8920 (t0) cc_final: 0.8670 (t0) REVERT: A 438 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8680 (t) REVERT: A 536 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 574 TYR cc_start: 0.9086 (p90) cc_final: 0.8864 (p90) REVERT: A 634 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8129 (ttt90) REVERT: C 202 MET cc_start: 0.8878 (ppp) cc_final: 0.8430 (tmm) REVERT: D 44 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7769 (pp30) REVERT: D 79 TYR cc_start: 0.8622 (m-80) cc_final: 0.8301 (m-10) REVERT: D 112 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8094 (tmm-80) REVERT: E 88 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7027 (tp40) REVERT: I 7 ARG cc_start: 0.8756 (mmt90) cc_final: 0.8017 (mmm-85) outliers start: 34 outliers final: 28 residues processed: 223 average time/residue: 0.2628 time to fit residues: 84.6443 Evaluate side-chains 230 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 260 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 A residue 766 ILE 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 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 315 THR Chi-restraints excluded: chain B residue 329 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.162637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107921 restraints weight = 16791.499| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.23 r_work: 0.2937 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2201 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= 0.149 Angle : 0.513 13.490 17820 Z= 0.268 Chirality : 0.043 0.139 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.095 16.997 1798 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.41 % Allowed : 12.48 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1616 helix: 2.08 (0.27), residues: 362 sheet: 0.32 (0.22), residues: 499 loop : 0.18 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 376 HIS 0.002 0.000 HIS D 102 PHE 0.016 0.001 PHE A 428 TYR 0.020 0.001 TYR A 296 ARG 0.008 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 591) hydrogen bonds : angle 4.71606 ( 1635) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.42844 ( 2) covalent geometry : bond 0.00334 (13128) covalent geometry : angle 0.51270 (17818) Misc. bond : bond 0.00044 ( 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 236 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1469 (mmp) cc_final: -0.1020 (mtt) REVERT: A 189 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 212 ARG cc_start: 0.8037 (ptt180) cc_final: 0.7683 (ptt180) REVERT: A 218 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: A 286 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8391 (tp40) REVERT: A 325 MET cc_start: 0.8341 (tpt) cc_final: 0.7580 (ppp) REVERT: A 338 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7635 (ttm-80) REVERT: A 422 ASN cc_start: 0.8868 (t0) cc_final: 0.8624 (t0) REVERT: A 438 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8697 (t) REVERT: A 440 PHE cc_start: 0.8072 (m-80) cc_final: 0.7306 (t80) REVERT: A 536 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 574 TYR cc_start: 0.9057 (p90) cc_final: 0.8833 (p90) REVERT: C 202 MET cc_start: 0.8886 (ppp) cc_final: 0.8447 (tmm) REVERT: D 44 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 79 TYR cc_start: 0.8574 (m-80) cc_final: 0.8309 (m-10) REVERT: E 88 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.7056 (tp40) REVERT: I 7 ARG cc_start: 0.8719 (mmt90) cc_final: 0.8008 (mmm-85) outliers start: 33 outliers final: 26 residues processed: 223 average time/residue: 0.2910 time to fit residues: 95.0176 Evaluate side-chains 230 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 260 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 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 766 ILE 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 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 315 THR 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 156 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.163403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108337 restraints weight = 16819.978| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.51 r_work: 0.2861 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2257 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= 0.120 Angle : 0.507 13.457 17820 Z= 0.264 Chirality : 0.043 0.137 1933 Planarity : 0.004 0.051 2341 Dihedral : 4.019 18.860 1798 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.04 % Allowed : 13.50 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1616 helix: 2.16 (0.27), residues: 362 sheet: 0.40 (0.22), residues: 491 loop : 0.20 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 PHE 0.018 0.001 PHE D 127 TYR 0.020 0.001 TYR A 296 ARG 0.014 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 591) hydrogen bonds : angle 4.61403 ( 1635) SS BOND : bond 0.00329 ( 1) SS BOND : angle 1.20569 ( 2) covalent geometry : bond 0.00266 (13128) covalent geometry : angle 0.50678 (17818) Misc. bond : bond 0.00033 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9927.26 seconds wall clock time: 172 minutes 42.38 seconds (10362.38 seconds total)