Starting phenix.real_space_refine on Thu Aug 6 07:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7e_41091/08_2026/8t7e_41091_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 79 5.16 5 C 8981 2.51 5 N 2512 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14273 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7158 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 60, 'TRANS': 847} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3188 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3166 Classifications: {'peptide': 400} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 394 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Conformer: "B" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 3.05, per 1000 atoms: 0.21 Number of scatterers: 14273 At special positions: 0 Unit cell: (105.728, 102.424, 142.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 37 15.00 O 2664 8.00 N 2512 7.00 C 8981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 508.4 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 34.9% alpha, 11.1% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.317A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.820A pdb=" N ALA A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.568A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 4.079A pdb=" N ASP A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.154A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.526A pdb=" N ALA A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.880A pdb=" N MET A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 793 through 809 removed outlier: 5.254A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 removed outlier: 3.766A pdb=" N TRP A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.367A pdb=" N THR A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 955 removed outlier: 4.308A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.505A pdb=" N ALA A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 980 Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.747A pdb=" N TYR A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1095 through 1115 Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.650A pdb=" N ASN A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.819A pdb=" N GLN B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.603A pdb=" N LYS B 176 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.888A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.894A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.883A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.603A pdb=" N THR B 447 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 448' Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.724A pdb=" N LEU C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.692A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 247 through 264 removed outlier: 3.655A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.542A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.897A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 479 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.536A pdb=" N VAL A 185 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 212 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 213 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.703A pdb=" N LEU A 435 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 884 through 890 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.209A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.844A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.138A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.997A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.39 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: 4252 1.34 - 1.46: 3109 1.46 - 1.58: 7144 1.58 - 1.70: 72 1.70 - 1.82: 125 Bond restraints: 14702 Sorted by residual: bond pdb=" C ILE A1069 " pdb=" N PRO A1070 " ideal model delta sigma weight residual 1.335 1.381 -0.046 8.70e-03 1.32e+04 2.75e+01 bond pdb=" C3' DT P 16 " pdb=" O3' DT P 16 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.40e+01 bond pdb=" C3' DG T 4 " pdb=" C2' DG T 4 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C1' DC P 20 " pdb=" N1 DC P 20 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C5' DT P 16 " pdb=" C4' DT P 16 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.26e+01 ... (remaining 14697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.21: 20016 6.21 - 12.42: 65 12.42 - 18.63: 4 18.63 - 24.84: 1 24.84 - 31.05: 4 Bond angle restraints: 20090 Sorted by residual: angle pdb=" O3' DC P 25 " pdb=" P DG P 26 " pdb=" OP2 DG P 26 " ideal model delta sigma weight residual 108.00 76.95 31.05 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OP1 DG P 26 " pdb=" P DG P 26 " pdb=" O5' DG P 26 " ideal model delta sigma weight residual 109.00 78.32 30.68 3.00e+00 1.11e-01 1.05e+02 angle pdb=" O3' DC P 25 " pdb=" P DG P 26 " pdb=" OP1 DG P 26 " ideal model delta sigma weight residual 108.00 80.15 27.85 3.00e+00 1.11e-01 8.62e+01 angle pdb=" OP1 DG P 26 " pdb=" P DG P 26 " pdb=" OP2 DG P 26 " ideal model delta sigma weight residual 120.00 145.39 -25.39 3.00e+00 1.11e-01 7.16e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.25 111.57 -8.32 1.05e+00 9.07e-01 6.28e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 8288 34.84 - 69.67: 344 69.67 - 104.51: 23 104.51 - 139.35: 2 139.35 - 174.19: 4 Dihedral angle restraints: 8661 sinusoidal: 3743 harmonic: 4918 Sorted by residual: dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PRO A 241 " pdb=" C PRO A 241 " pdb=" N ALA A 242 " pdb=" CA ALA A 242 " ideal model delta harmonic sigma weight residual 180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA PRO A 745 " pdb=" C PRO A 745 " pdb=" N GLY A 746 " pdb=" CA GLY A 746 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 8658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2071 0.118 - 0.236: 109 0.236 - 0.354: 3 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 2184 Sorted by residual: chirality pdb=" P DG P 26 " pdb=" OP1 DG P 26 " pdb=" OP2 DG P 26 " pdb=" O5' DG P 26 " both_signs ideal model delta sigma weight residual True 2.34 1.75 0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE A1185 " pdb=" CA ILE A1185 " pdb=" CG1 ILE A1185 " pdb=" CG2 ILE A1185 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2181 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 309 " -0.663 9.50e-02 1.11e+02 2.97e-01 5.38e+01 pdb=" NE ARG A 309 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 309 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 309 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 309 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 389 " 0.543 9.50e-02 1.11e+02 2.44e-01 3.62e+01 pdb=" NE ARG B 389 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 389 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 389 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 389 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 139 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 140 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " 0.044 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3615 2.81 - 3.33: 12917 3.33 - 3.86: 24734 3.86 - 4.38: 28176 4.38 - 4.90: 45888 Nonbonded interactions: 115330 Sorted by model distance: nonbonded pdb=" OH TYR C 193 " pdb=" O LEU C 322 " model vdw 2.288 3.040 nonbonded pdb=" OG SER B 457 " pdb=" O THR B 460 " model vdw 2.327 3.040 nonbonded pdb=" O PRO B 244 " pdb=" OG SER B 248 " model vdw 2.337 3.040 nonbonded pdb=" O SER A 615 " pdb=" NZ LYS A 751 " model vdw 2.337 3.120 nonbonded pdb=" O GLU A 447 " pdb=" OG1 THR A 451 " model vdw 2.337 3.040 ... (remaining 115325 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 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or (r \ esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219 \ or resid 229 through 283 or (resid 284 and (name N or name CA or name C or name \ O or name CB )) or resid 285 through 327 or (resid 328 and (name N or name CA or \ name C or name O or name CB )) or resid 329 through 355 or resid 368 through 48 \ 5)) selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ rough 485)) } 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=0.00 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14702 Z= 0.311 Angle : 1.106 31.048 20090 Z= 0.587 Chirality : 0.057 0.590 2184 Planarity : 0.011 0.297 2452 Dihedral : 18.219 174.187 5483 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.62 % Favored : 92.26 % Rotamer: Outliers : 0.69 % Allowed : 8.54 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.18), residues: 1680 helix: -1.93 (0.17), residues: 589 sheet: -0.58 (0.34), residues: 220 loop : -2.35 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1187 TYR 0.033 0.002 TYR A 150 PHE 0.025 0.002 PHE A 197 TRP 0.026 0.002 TRP C 241 HIS 0.011 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.31 (14702) covalent geometry : angle 1.10584 / 0.59 (20090) hydrogen bonds : bond 0.14702 / 10.31 ( 507) hydrogen bonds : angle 7.30120 / 5.17 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 298 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 457 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6571 (ptp-170) REVERT: A 544 MET cc_start: 0.7305 (ppp) cc_final: 0.6993 (ppp) REVERT: A 812 MET cc_start: 0.5800 (ppp) cc_final: 0.5520 (ptm) REVERT: A 907 PHE cc_start: 0.7592 (t80) cc_final: 0.7344 (t80) REVERT: A 970 ASN cc_start: 0.6988 (t0) cc_final: 0.6770 (t0) REVERT: A 1079 ILE cc_start: 0.6772 (tt) cc_final: 0.6343 (tt) REVERT: A 1170 LEU cc_start: 0.6554 (pt) cc_final: 0.6294 (pp) REVERT: B 74 GLN cc_start: 0.7411 (mp10) cc_final: 0.7161 (mp10) REVERT: C 325 ARG cc_start: 0.6100 (tpp-160) cc_final: 0.5768 (tpp-160) REVERT: C 400 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7075 (tm-30) outliers start: 10 outliers final: 2 residues processed: 306 average time/residue: 0.1189 time to fit residues: 52.2589 Evaluate side-chains 199 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 920 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 354 ASN A 390 GLN A 409 GLN A 440 ASN A 472 GLN A 565 HIS A 803 ASN A 879 GLN A 959 GLN A 968 GLN A 970 ASN A1089 GLN B 77 HIS B 84 GLN B 85 GLN B 201 ASN B 249 ASN B 272 ASN B 287 ASN B 313 HIS B 400 GLN B 404 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 454 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.191689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.149731 restraints weight = 25499.040| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.00 r_work: 0.3862 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14702 Z= 0.145 Angle : 0.819 36.490 20090 Z= 0.389 Chirality : 0.047 0.517 2184 Planarity : 0.005 0.071 2452 Dihedral : 17.385 172.228 2232 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 1.87 % Allowed : 14.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.19), residues: 1680 helix: -0.64 (0.20), residues: 586 sheet: -0.46 (0.35), residues: 207 loop : -2.08 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1187 TYR 0.018 0.002 TYR A 434 PHE 0.017 0.001 PHE A 377 TRP 0.024 0.001 TRP A1118 HIS 0.012 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14702) covalent geometry : angle 0.81923 / 0.39 (20090) hydrogen bonds : bond 0.04661 / 3.15 ( 507) hydrogen bonds : angle 5.51139 / 3.93 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6362 (pp30) cc_final: 0.6124 (pp30) REVERT: A 544 MET cc_start: 0.7676 (ppp) cc_final: 0.7424 (ppp) REVERT: A 744 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8256 (mm) REVERT: A 907 PHE cc_start: 0.8078 (t80) cc_final: 0.6953 (t80) REVERT: A 1093 MET cc_start: 0.5658 (tpt) cc_final: 0.4745 (ptp) REVERT: B 74 GLN cc_start: 0.7474 (mp10) cc_final: 0.7198 (mp10) REVERT: C 156 ILE cc_start: 0.6031 (pt) cc_final: 0.5828 (pt) REVERT: C 400 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 466 MET cc_start: 0.7638 (ttm) cc_final: 0.7220 (ttt) outliers start: 27 outliers final: 12 residues processed: 242 average time/residue: 0.1214 time to fit residues: 42.9757 Evaluate side-chains 216 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 146 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 564 GLN A 959 GLN B 313 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.186669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143524 restraints weight = 26398.742| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.01 r_work: 0.3760 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14702 Z= 0.187 Angle : 0.713 10.971 20090 Z= 0.362 Chirality : 0.046 0.299 2184 Planarity : 0.005 0.054 2452 Dihedral : 17.315 170.988 2231 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 2.50 % Allowed : 15.61 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1680 helix: -0.09 (0.21), residues: 599 sheet: -0.81 (0.33), residues: 223 loop : -2.01 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1187 TYR 0.021 0.002 TYR A 434 PHE 0.021 0.002 PHE B 266 TRP 0.023 0.002 TRP A 312 HIS 0.009 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (14702) covalent geometry : angle 0.71329 / 0.36 (20090) hydrogen bonds : bond 0.04388 / 2.93 ( 507) hydrogen bonds : angle 5.17401 / 3.67 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.3224 (m-80) cc_final: 0.2794 (m-80) REVERT: A 382 MET cc_start: 0.1790 (tpt) cc_final: 0.1491 (tpt) REVERT: A 386 ARG cc_start: 0.6591 (mmp80) cc_final: 0.6345 (mmp80) REVERT: A 544 MET cc_start: 0.7884 (ppp) cc_final: 0.7572 (ppp) REVERT: A 550 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 594 LEU cc_start: 0.6810 (tp) cc_final: 0.6518 (tt) REVERT: A 744 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 907 PHE cc_start: 0.8198 (t80) cc_final: 0.7134 (t80) REVERT: A 964 ARG cc_start: 0.6389 (mpt90) cc_final: 0.6145 (mpt180) REVERT: A 1093 MET cc_start: 0.5614 (tpt) cc_final: 0.4664 (ptp) REVERT: A 1116 MET cc_start: 0.6707 (mtm) cc_final: 0.6504 (mtm) REVERT: C 219 PHE cc_start: 0.6773 (m-10) cc_final: 0.6538 (m-10) REVERT: C 325 ARG cc_start: 0.6238 (tpp-160) cc_final: 0.5644 (tpp-160) REVERT: C 400 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7313 (tm-30) outliers start: 36 outliers final: 24 residues processed: 238 average time/residue: 0.1123 time to fit residues: 39.4541 Evaluate side-chains 221 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 0.0570 chunk 14 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 149 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 GLN A 959 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.188852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.145844 restraints weight = 26103.720| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.01 r_work: 0.3811 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14702 Z= 0.128 Angle : 0.664 12.425 20090 Z= 0.335 Chirality : 0.044 0.302 2184 Planarity : 0.004 0.051 2452 Dihedral : 17.275 171.204 2231 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 2.36 % Allowed : 17.56 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1680 helix: 0.29 (0.22), residues: 593 sheet: -0.72 (0.33), residues: 214 loop : -1.90 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.017 0.001 TYR A 434 PHE 0.013 0.001 PHE B 403 TRP 0.025 0.001 TRP A 312 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14702) covalent geometry : angle 0.66356 / 0.34 (20090) hydrogen bonds : bond 0.03818 / 2.55 ( 507) hydrogen bonds : angle 4.90964 / 3.49 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ARG cc_start: 0.6534 (mmp80) cc_final: 0.6267 (mmp80) REVERT: A 454 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 544 MET cc_start: 0.7781 (ppp) cc_final: 0.7419 (ppp) REVERT: A 594 LEU cc_start: 0.6805 (tp) cc_final: 0.6539 (tt) REVERT: A 744 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 907 PHE cc_start: 0.8163 (t80) cc_final: 0.6960 (t80) REVERT: A 955 TYR cc_start: 0.7446 (m-80) cc_final: 0.7119 (m-80) REVERT: A 964 ARG cc_start: 0.6370 (mpt90) cc_final: 0.6111 (mpt180) REVERT: A 1093 MET cc_start: 0.5527 (tpt) cc_final: 0.4791 (ptp) REVERT: A 1116 MET cc_start: 0.6655 (mtm) cc_final: 0.6272 (mtm) REVERT: C 281 GLU cc_start: 0.7646 (mp0) cc_final: 0.7398 (pp20) REVERT: C 400 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7224 (tm-30) REVERT: C 479 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6648 (pt) outliers start: 34 outliers final: 23 residues processed: 237 average time/residue: 0.1049 time to fit residues: 37.2535 Evaluate side-chains 232 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 34 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 60 optimal weight: 0.0270 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 0.7654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** 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 = 0.4469 r_free = 0.4469 target = 0.188010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.145021 restraints weight = 25612.067| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.95 r_work: 0.3788 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14702 Z= 0.131 Angle : 0.657 11.892 20090 Z= 0.333 Chirality : 0.044 0.293 2184 Planarity : 0.004 0.066 2452 Dihedral : 17.178 171.279 2231 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 2.98 % Allowed : 18.04 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1680 helix: 0.52 (0.22), residues: 591 sheet: -0.73 (0.33), residues: 219 loop : -1.83 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 597 TYR 0.013 0.001 TYR B 193 PHE 0.019 0.001 PHE A 961 TRP 0.027 0.001 TRP A 312 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14702) covalent geometry : angle 0.65712 / 0.33 (20090) hydrogen bonds : bond 0.03746 / 2.51 ( 507) hydrogen bonds : angle 4.80885 / 3.42 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.2908 (m-80) cc_final: 0.2568 (m-80) REVERT: A 544 MET cc_start: 0.7758 (ppp) cc_final: 0.7396 (ppp) REVERT: A 594 LEU cc_start: 0.6843 (tp) cc_final: 0.6565 (tt) REVERT: A 744 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 907 PHE cc_start: 0.8116 (t80) cc_final: 0.6972 (t80) REVERT: A 955 TYR cc_start: 0.7450 (m-80) cc_final: 0.7114 (m-80) REVERT: A 964 ARG cc_start: 0.6434 (mpt90) cc_final: 0.6160 (mpt180) REVERT: A 1093 MET cc_start: 0.5291 (tpt) cc_final: 0.4725 (ptp) REVERT: A 1153 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7299 (tt) REVERT: C 400 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 479 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6628 (pt) outliers start: 43 outliers final: 30 residues processed: 240 average time/residue: 0.1040 time to fit residues: 38.0798 Evaluate side-chains 232 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 131 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 142 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 16 optimal weight: 0.0070 chunk 135 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.188468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.146831 restraints weight = 26017.964| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.22 r_work: 0.3783 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14702 Z= 0.125 Angle : 0.659 11.859 20090 Z= 0.331 Chirality : 0.044 0.288 2184 Planarity : 0.004 0.054 2452 Dihedral : 17.132 171.550 2231 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 2.85 % Allowed : 19.01 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.21), residues: 1680 helix: 0.60 (0.22), residues: 590 sheet: -0.51 (0.34), residues: 209 loop : -1.83 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 597 TYR 0.018 0.001 TYR A 434 PHE 0.016 0.001 PHE A 610 TRP 0.031 0.001 TRP A 312 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14702) covalent geometry : angle 0.65888 / 0.33 (20090) hydrogen bonds : bond 0.03588 / 2.41 ( 507) hydrogen bonds : angle 4.69124 / 3.34 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.3143 (m-80) cc_final: 0.2676 (m-80) REVERT: A 544 MET cc_start: 0.7812 (ppp) cc_final: 0.7487 (ppp) REVERT: A 594 LEU cc_start: 0.6853 (tp) cc_final: 0.6565 (tt) REVERT: A 744 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 907 PHE cc_start: 0.8190 (t80) cc_final: 0.6950 (t80) REVERT: A 955 TYR cc_start: 0.7528 (m-80) cc_final: 0.7223 (m-80) REVERT: A 964 ARG cc_start: 0.6364 (mpt90) cc_final: 0.6081 (mpt180) REVERT: A 1093 MET cc_start: 0.5357 (tpt) cc_final: 0.4808 (ptt) REVERT: A 1112 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6846 (mtp) REVERT: A 1116 MET cc_start: 0.6496 (mtm) cc_final: 0.6257 (mtt) REVERT: A 1153 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7402 (tt) REVERT: C 400 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 479 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6545 (pt) outliers start: 41 outliers final: 27 residues processed: 233 average time/residue: 0.1031 time to fit residues: 36.7282 Evaluate side-chains 228 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 911 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137223 restraints weight = 25127.272| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.90 r_work: 0.3681 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14702 Z= 0.262 Angle : 0.771 13.294 20090 Z= 0.394 Chirality : 0.048 0.297 2184 Planarity : 0.005 0.052 2452 Dihedral : 17.173 171.559 2231 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 3.61 % Allowed : 18.81 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1680 helix: 0.18 (0.21), residues: 607 sheet: -0.84 (0.34), residues: 219 loop : -2.10 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 227 TYR 0.023 0.003 TYR A 434 PHE 0.026 0.002 PHE B 266 TRP 0.034 0.002 TRP A 312 HIS 0.009 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.26 (14702) covalent geometry : angle 0.77052 / 0.39 (20090) hydrogen bonds : bond 0.04543 / 3.06 ( 507) hydrogen bonds : angle 5.04692 / 3.58 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6799 (pp30) cc_final: 0.6484 (pp30) REVERT: A 304 LEU cc_start: 0.6729 (mm) cc_final: 0.6519 (mm) REVERT: A 544 MET cc_start: 0.7993 (ppp) cc_final: 0.7688 (ppp) REVERT: A 594 LEU cc_start: 0.7024 (tp) cc_final: 0.6768 (tt) REVERT: A 744 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 907 PHE cc_start: 0.8313 (t80) cc_final: 0.7066 (t80) REVERT: A 955 TYR cc_start: 0.7659 (m-80) cc_final: 0.7452 (m-80) REVERT: A 964 ARG cc_start: 0.6592 (mpt90) cc_final: 0.6306 (mpt180) REVERT: A 1093 MET cc_start: 0.5275 (tpt) cc_final: 0.4711 (ptt) REVERT: A 1108 TYR cc_start: 0.7752 (t80) cc_final: 0.7353 (t80) REVERT: A 1112 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7378 (mpp) REVERT: C 325 ARG cc_start: 0.6201 (tpp-160) cc_final: 0.4941 (tpt170) REVERT: C 400 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 466 MET cc_start: 0.7734 (ttm) cc_final: 0.7460 (ttm) REVERT: C 479 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6847 (pt) outliers start: 52 outliers final: 33 residues processed: 238 average time/residue: 0.1144 time to fit residues: 40.3833 Evaluate side-chains 222 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 100 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS A 959 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 = 0.4424 r_free = 0.4424 target = 0.183881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140537 restraints weight = 25133.660| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.89 r_work: 0.3725 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14702 Z= 0.152 Angle : 0.692 12.317 20090 Z= 0.352 Chirality : 0.045 0.272 2184 Planarity : 0.004 0.050 2452 Dihedral : 17.153 172.498 2231 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 2.85 % Allowed : 19.99 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1680 helix: 0.42 (0.22), residues: 599 sheet: -0.80 (0.34), residues: 219 loop : -1.96 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 101 TYR 0.021 0.001 TYR A 986 PHE 0.013 0.001 PHE A 610 TRP 0.035 0.001 TRP A 312 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14702) covalent geometry : angle 0.69193 / 0.35 (20090) hydrogen bonds : bond 0.03861 / 2.58 ( 507) hydrogen bonds : angle 4.83760 / 3.45 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6869 (pp30) cc_final: 0.6505 (pp30) REVERT: A 465 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: A 544 MET cc_start: 0.7937 (ppp) cc_final: 0.7621 (ppp) REVERT: A 594 LEU cc_start: 0.6977 (tp) cc_final: 0.6709 (tt) REVERT: A 615 SER cc_start: 0.4905 (OUTLIER) cc_final: 0.3127 (m) REVERT: A 907 PHE cc_start: 0.8307 (t80) cc_final: 0.7052 (t80) REVERT: A 964 ARG cc_start: 0.6532 (mpt90) cc_final: 0.6250 (mpt180) REVERT: A 1093 MET cc_start: 0.5198 (tpt) cc_final: 0.4771 (ptt) REVERT: A 1108 TYR cc_start: 0.7691 (t80) cc_final: 0.7385 (t80) REVERT: A 1214 GLN cc_start: 0.6078 (tm-30) cc_final: 0.5715 (tm-30) REVERT: B 256 LEU cc_start: 0.8599 (tt) cc_final: 0.8054 (tt) REVERT: C 325 ARG cc_start: 0.6081 (tpp-160) cc_final: 0.4766 (tpt170) REVERT: C 400 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7171 (tm-30) REVERT: C 466 MET cc_start: 0.7571 (ttm) cc_final: 0.7212 (ttm) REVERT: C 479 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6679 (pt) outliers start: 41 outliers final: 31 residues processed: 229 average time/residue: 0.1021 time to fit residues: 35.5010 Evaluate side-chains 229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 146 optimal weight: 0.0020 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** 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 = 0.4430 r_free = 0.4430 target = 0.184375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140923 restraints weight = 25184.215| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.92 r_work: 0.3731 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14702 Z= 0.147 Angle : 0.686 11.723 20090 Z= 0.348 Chirality : 0.045 0.266 2184 Planarity : 0.004 0.051 2452 Dihedral : 17.118 172.139 2231 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.98 % Favored : 91.90 % Rotamer: Outliers : 2.71 % Allowed : 20.47 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1680 helix: 0.50 (0.22), residues: 607 sheet: -0.75 (0.34), residues: 219 loop : -1.94 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 597 TYR 0.038 0.002 TYR A1108 PHE 0.023 0.001 PHE A 961 TRP 0.042 0.001 TRP A 312 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (14702) covalent geometry : angle 0.68646 / 0.35 (20090) hydrogen bonds : bond 0.03810 / 2.55 ( 507) hydrogen bonds : angle 4.79536 / 3.41 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6862 (pp30) cc_final: 0.6488 (pp30) REVERT: A 544 MET cc_start: 0.7937 (ppp) cc_final: 0.7636 (ppp) REVERT: A 615 SER cc_start: 0.4990 (OUTLIER) cc_final: 0.3223 (m) REVERT: A 907 PHE cc_start: 0.8332 (t80) cc_final: 0.7160 (t80) REVERT: A 964 ARG cc_start: 0.6519 (mpt90) cc_final: 0.6237 (mpt180) REVERT: A 1093 MET cc_start: 0.5251 (tpt) cc_final: 0.4859 (ptt) REVERT: A 1094 THR cc_start: 0.6828 (p) cc_final: 0.6556 (t) REVERT: A 1170 LEU cc_start: 0.6810 (pp) cc_final: 0.6507 (pp) REVERT: A 1214 GLN cc_start: 0.6036 (tm-30) cc_final: 0.5689 (tm-30) REVERT: B 256 LEU cc_start: 0.8592 (tt) cc_final: 0.8033 (tt) REVERT: C 325 ARG cc_start: 0.6073 (tpp-160) cc_final: 0.4786 (tpt170) REVERT: C 400 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7149 (tm-30) REVERT: C 479 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6644 (pt) outliers start: 39 outliers final: 30 residues processed: 233 average time/residue: 0.0967 time to fit residues: 34.2268 Evaluate side-chains 229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 906 HIS B 84 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** 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 = 0.4435 r_free = 0.4435 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141617 restraints weight = 25446.250| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.95 r_work: 0.3738 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14702 Z= 0.142 Angle : 0.694 11.668 20090 Z= 0.350 Chirality : 0.045 0.266 2184 Planarity : 0.004 0.051 2452 Dihedral : 17.092 172.173 2231 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.98 % Favored : 91.90 % Rotamer: Outliers : 2.57 % Allowed : 20.89 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1680 helix: 0.48 (0.22), residues: 606 sheet: -0.73 (0.34), residues: 219 loop : -1.91 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 597 TYR 0.044 0.002 TYR A1108 PHE 0.028 0.001 PHE A 961 TRP 0.046 0.001 TRP A 312 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14702) covalent geometry : angle 0.69439 / 0.35 (20090) hydrogen bonds : bond 0.03740 / 2.51 ( 507) hydrogen bonds : angle 4.78312 / 3.39 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6802 (pp30) cc_final: 0.6508 (pp30) REVERT: A 544 MET cc_start: 0.7888 (ppp) cc_final: 0.7593 (ppp) REVERT: A 615 SER cc_start: 0.4863 (OUTLIER) cc_final: 0.3054 (m) REVERT: A 907 PHE cc_start: 0.8308 (t80) cc_final: 0.7147 (t80) REVERT: A 955 TYR cc_start: 0.7574 (m-80) cc_final: 0.6931 (m-80) REVERT: A 964 ARG cc_start: 0.6514 (mpt90) cc_final: 0.6230 (mpt180) REVERT: A 1093 MET cc_start: 0.5274 (tpt) cc_final: 0.4862 (ptt) REVERT: A 1094 THR cc_start: 0.6857 (p) cc_final: 0.6566 (t) REVERT: A 1214 GLN cc_start: 0.6042 (tm-30) cc_final: 0.5699 (tm-30) REVERT: B 256 LEU cc_start: 0.8611 (tt) cc_final: 0.8051 (tt) REVERT: C 325 ARG cc_start: 0.6095 (tpp-160) cc_final: 0.4781 (tpt170) REVERT: C 400 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7135 (tm-30) REVERT: C 479 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6671 (pt) outliers start: 37 outliers final: 32 residues processed: 228 average time/residue: 0.1028 time to fit residues: 35.4612 Evaluate side-chains 231 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 906 HIS Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 132 optimal weight: 0.0980 chunk 157 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 906 HIS ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** 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 = 0.4438 r_free = 0.4438 target = 0.185317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.141861 restraints weight = 26376.138| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.03 r_work: 0.3742 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.135 Angle : 0.691 11.281 20090 Z= 0.348 Chirality : 0.045 0.264 2184 Planarity : 0.004 0.051 2452 Dihedral : 17.054 172.122 2231 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 2.85 % Allowed : 20.89 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1680 helix: 0.55 (0.22), residues: 599 sheet: -0.71 (0.34), residues: 219 loop : -1.89 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 275 TYR 0.037 0.002 TYR A1108 PHE 0.027 0.001 PHE A 961 TRP 0.046 0.001 TRP A 312 HIS 0.021 0.001 HIS A 906 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14702) covalent geometry : angle 0.69091 / 0.35 (20090) hydrogen bonds : bond 0.03749 / 2.51 ( 507) hydrogen bonds : angle 4.74643 / 3.35 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.78 seconds wall clock time: 64 minutes 29.72 seconds (3869.72 seconds total)