Starting phenix.real_space_refine on Mon Dec 30 23:01:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7e_41091/12_2024/8t7e_41091_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7e_41091/12_2024/8t7e_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_41091/12_2024/8t7e_41091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7e_41091/12_2024/8t7e_41091.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7e_41091/12_2024/8t7e_41091_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7e_41091/12_2024/8t7e_41091_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 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: 8.92, per 1000 atoms: 0.62 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: 3.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.03 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: 4.93 Time building geometry restraints manager: 4.08 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=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.63e+00 bond pdb=" C3' DT P 16 " pdb=" O3' DT P 16 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.53e+00 bond pdb=" N GLY B 390 " pdb=" CA GLY B 390 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.48e+00 bond pdb=" N GLY B 388 " pdb=" CA GLY B 388 " ideal model delta sigma weight residual 1.446 1.479 -0.033 1.30e-02 5.92e+03 6.38e+00 ... (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 - 0.120: 2084 0.120 - 0.240: 96 0.240 - 0.360: 3 0.360 - 0.480: 0 0.480 - 0.600: 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 2.35 1.75 0.60 2.00e-01 2.50e+01 8.99e+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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.260 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 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 0.077 14702 Z= 0.290 Angle : 1.092 31.048 20090 Z= 0.543 Chirality : 0.056 0.600 2184 Planarity : 0.011 0.297 2452 Dihedral : 18.219 174.187 5483 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP C 241 HIS 0.011 0.001 HIS C 454 PHE 0.025 0.002 PHE A 197 TYR 0.033 0.002 TYR A 150 ARG 0.009 0.001 ARG A1187 *********************** 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 : 1.616 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: 0.6768 (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: 0.2997 time to fit residues: 129.6176 Evaluate side-chains 198 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 144 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 ASN A 354 ASN A 390 GLN A 409 GLN A 440 ASN A 472 GLN A 564 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 313 HIS B 400 GLN B 404 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 318 ASN C 454 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14702 Z= 0.244 Angle : 0.733 22.277 20090 Z= 0.367 Chirality : 0.063 2.108 2184 Planarity : 0.005 0.065 2452 Dihedral : 17.336 173.850 2232 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.74 % Favored : 92.14 % Rotamer: Outliers : 1.87 % Allowed : 14.71 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1680 helix: -0.48 (0.21), residues: 593 sheet: -0.58 (0.35), residues: 215 loop : -2.06 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1118 HIS 0.011 0.001 HIS C 258 PHE 0.018 0.002 PHE B 266 TYR 0.017 0.002 TYR A 150 ARG 0.009 0.001 ARG A1187 *********************** 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 241 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7372 (ppp) cc_final: 0.7129 (ppp) REVERT: A 744 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 907 PHE cc_start: 0.7633 (t80) cc_final: 0.6911 (t80) REVERT: A 1093 MET cc_start: 0.5095 (tpt) cc_final: 0.4435 (ptp) REVERT: B 74 GLN cc_start: 0.7603 (mp10) cc_final: 0.7317 (mp10) REVERT: C 156 ILE cc_start: 0.4521 (pt) cc_final: 0.4217 (pt) REVERT: C 400 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7436 (tm-30) outliers start: 27 outliers final: 13 residues processed: 232 average time/residue: 0.2778 time to fit residues: 93.7960 Evaluate side-chains 212 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 308 ASP 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 86 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 540 GLN A 550 GLN A 894 GLN A 911 HIS A 959 GLN B 216 HIS ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 323 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 14702 Z= 0.459 Angle : 0.826 13.043 20090 Z= 0.422 Chirality : 0.048 0.192 2184 Planarity : 0.006 0.064 2452 Dihedral : 17.468 173.223 2231 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 3.96 % Allowed : 16.17 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.19), residues: 1680 helix: -0.35 (0.21), residues: 605 sheet: -0.92 (0.33), residues: 220 loop : -2.21 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 312 HIS 0.011 0.002 HIS C 258 PHE 0.033 0.003 PHE B 266 TYR 0.025 0.003 TYR A 434 ARG 0.009 0.001 ARG C 325 *********************** 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 276 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 THR cc_start: 0.6133 (OUTLIER) cc_final: 0.5746 (m) REVERT: A 345 TRP cc_start: 0.5190 (m-90) cc_final: 0.3523 (t-100) REVERT: A 544 MET cc_start: 0.7795 (ppp) cc_final: 0.7466 (ppp) REVERT: A 550 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: A 744 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 907 PHE cc_start: 0.7911 (t80) cc_final: 0.6998 (t80) REVERT: A 1093 MET cc_start: 0.5066 (tpt) cc_final: 0.4669 (ptp) REVERT: B 74 GLN cc_start: 0.7881 (mp10) cc_final: 0.7645 (mp10) REVERT: B 122 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6897 (tpp80) REVERT: C 256 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7712 (tp) REVERT: C 400 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 479 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6785 (pt) outliers start: 57 outliers final: 38 residues processed: 256 average time/residue: 0.2861 time to fit residues: 107.3344 Evaluate side-chains 229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 245 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 552 LEU 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 605 LEU 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 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 844 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 1112 MET Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 122 ARG 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 B residue 427 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 0.0270 chunk 156 optimal weight: 0.0570 chunk 165 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 44 optimal weight: 0.0010 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 950 ASN A 959 GLN B 124 GLN B 305 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14702 Z= 0.182 Angle : 0.688 14.405 20090 Z= 0.343 Chirality : 0.043 0.222 2184 Planarity : 0.004 0.051 2452 Dihedral : 17.329 174.725 2231 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 2.91 % Allowed : 18.53 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1680 helix: 0.28 (0.22), residues: 597 sheet: -0.76 (0.33), residues: 209 loop : -2.02 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 312 HIS 0.004 0.001 HIS C 258 PHE 0.018 0.001 PHE B 403 TYR 0.021 0.001 TYR A1108 ARG 0.007 0.000 ARG C 325 *********************** 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 266 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.5079 (m-90) cc_final: 0.3541 (t-100) REVERT: A 544 MET cc_start: 0.7592 (ppp) cc_final: 0.7230 (ppp) REVERT: A 550 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: A 559 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4862 (mt) REVERT: A 812 MET cc_start: 0.6652 (ppp) cc_final: 0.5831 (ptm) REVERT: A 907 PHE cc_start: 0.7821 (t80) cc_final: 0.6952 (t80) REVERT: A 1093 MET cc_start: 0.4852 (tpt) cc_final: 0.4648 (ptp) REVERT: A 1128 ARG cc_start: 0.6013 (mmm160) cc_final: 0.5726 (mmt-90) REVERT: C 256 LEU cc_start: 0.7807 (tt) cc_final: 0.7521 (tp) REVERT: C 400 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7400 (tm-30) outliers start: 42 outliers final: 24 residues processed: 255 average time/residue: 0.2669 time to fit residues: 100.8771 Evaluate side-chains 224 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 550 GLN Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU 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 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 B residue 425 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 754 HIS A 959 GLN B 313 HIS B 368 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14702 Z= 0.336 Angle : 0.742 14.461 20090 Z= 0.376 Chirality : 0.045 0.183 2184 Planarity : 0.005 0.051 2452 Dihedral : 17.264 174.462 2231 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 3.61 % Allowed : 19.36 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1680 helix: 0.16 (0.22), residues: 602 sheet: -0.94 (0.33), residues: 219 loop : -2.05 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 312 HIS 0.008 0.001 HIS B 313 PHE 0.023 0.002 PHE A 961 TYR 0.027 0.002 TYR B 432 ARG 0.007 0.001 ARG A 972 *********************** 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 259 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.5271 (m-90) cc_final: 0.3577 (t-100) REVERT: A 356 LEU cc_start: 0.3185 (OUTLIER) cc_final: 0.2829 (tt) REVERT: A 377 PHE cc_start: 0.4761 (t80) cc_final: 0.4431 (t80) REVERT: A 544 MET cc_start: 0.7658 (ppp) cc_final: 0.7347 (ppp) REVERT: A 550 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: A 907 PHE cc_start: 0.7994 (t80) cc_final: 0.7098 (t80) REVERT: A 1093 MET cc_start: 0.4875 (tpt) cc_final: 0.4662 (ptp) REVERT: A 1128 ARG cc_start: 0.6246 (mmm160) cc_final: 0.5956 (mmt-90) REVERT: B 74 GLN cc_start: 0.7759 (mp10) cc_final: 0.7468 (mp10) REVERT: C 256 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7693 (tp) REVERT: C 400 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 479 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6571 (pt) outliers start: 52 outliers final: 31 residues processed: 244 average time/residue: 0.2568 time to fit residues: 93.2168 Evaluate side-chains 231 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 130 LEU 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 356 LEU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 778 THR 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 243 THR Chi-restraints excluded: chain B residue 261 GLN 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 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 256 LEU Chi-restraints excluded: chain C residue 338 VAL 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 55 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 959 GLN B 368 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14702 Z= 0.230 Angle : 0.692 13.245 20090 Z= 0.349 Chirality : 0.044 0.188 2184 Planarity : 0.004 0.050 2452 Dihedral : 17.227 175.108 2231 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 3.75 % Allowed : 19.50 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1680 helix: 0.32 (0.22), residues: 599 sheet: -0.92 (0.33), residues: 219 loop : -1.97 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 312 HIS 0.004 0.001 HIS C 258 PHE 0.013 0.001 PHE B 403 TYR 0.024 0.002 TYR B 432 ARG 0.005 0.000 ARG A 562 *********************** 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 259 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.5127 (m-90) cc_final: 0.3476 (t-100) REVERT: A 356 LEU cc_start: 0.3296 (OUTLIER) cc_final: 0.2979 (tt) REVERT: A 377 PHE cc_start: 0.4744 (t80) cc_final: 0.4451 (t80) REVERT: A 550 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: A 615 SER cc_start: 0.4776 (OUTLIER) cc_final: 0.2848 (m) REVERT: A 812 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6067 (ptm) REVERT: A 907 PHE cc_start: 0.7947 (t80) cc_final: 0.7054 (t80) REVERT: A 1128 ARG cc_start: 0.5964 (mmm160) cc_final: 0.5615 (mmt-90) REVERT: B 74 GLN cc_start: 0.7668 (mp10) cc_final: 0.7070 (mp10) REVERT: C 197 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7727 (tt) REVERT: C 256 LEU cc_start: 0.7970 (tt) cc_final: 0.7673 (tp) REVERT: C 400 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7356 (tm-30) REVERT: C 479 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6421 (pt) outliers start: 54 outliers final: 28 residues processed: 249 average time/residue: 0.2520 time to fit residues: 93.3311 Evaluate side-chains 226 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 130 LEU 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 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 550 GLN 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 792 LEU Chi-restraints excluded: chain A residue 812 MET 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 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 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 197 LEU Chi-restraints excluded: chain C residue 238 SER 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 159 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 906 HIS A 959 GLN B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3439 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= 0.194 Angle : 0.677 12.294 20090 Z= 0.341 Chirality : 0.043 0.177 2184 Planarity : 0.004 0.049 2452 Dihedral : 17.148 174.663 2231 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 2.71 % Allowed : 21.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1680 helix: 0.49 (0.22), residues: 594 sheet: -0.70 (0.33), residues: 215 loop : -1.96 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 312 HIS 0.008 0.001 HIS A 906 PHE 0.022 0.002 PHE A 961 TYR 0.021 0.001 TYR B 432 ARG 0.005 0.000 ARG A 972 *********************** 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 245 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.4603 (t80) cc_final: 0.4387 (t80) REVERT: A 550 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 615 SER cc_start: 0.4765 (OUTLIER) cc_final: 0.2812 (m) REVERT: A 812 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6037 (ptm) REVERT: A 907 PHE cc_start: 0.7938 (t80) cc_final: 0.7104 (t80) REVERT: A 955 TYR cc_start: 0.7328 (m-80) cc_final: 0.6788 (m-80) REVERT: A 1128 ARG cc_start: 0.5896 (mmm160) cc_final: 0.5486 (mmt-90) REVERT: B 74 GLN cc_start: 0.7609 (mp10) cc_final: 0.7235 (mp10) REVERT: C 197 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7583 (tt) REVERT: C 256 LEU cc_start: 0.7940 (tt) cc_final: 0.7613 (tp) REVERT: C 400 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 479 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6415 (pt) outliers start: 39 outliers final: 26 residues processed: 237 average time/residue: 0.2703 time to fit residues: 97.5140 Evaluate side-chains 229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 130 LEU 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 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 920 THR 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 387 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 SER 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 101 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 HIS B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3514 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= 0.203 Angle : 0.682 12.022 20090 Z= 0.342 Chirality : 0.043 0.244 2184 Planarity : 0.004 0.048 2452 Dihedral : 17.085 174.658 2231 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.73 % Rotamer: Outliers : 2.91 % Allowed : 20.96 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1680 helix: 0.53 (0.22), residues: 595 sheet: -0.64 (0.34), residues: 215 loop : -1.93 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 312 HIS 0.015 0.001 HIS C 258 PHE 0.024 0.001 PHE A 961 TYR 0.015 0.001 TYR A 434 ARG 0.005 0.000 ARG B 325 *********************** 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 244 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 GLN cc_start: 0.7367 (tm-30) cc_final: 0.7029 (tm-30) REVERT: A 615 SER cc_start: 0.4723 (OUTLIER) cc_final: 0.2793 (m) REVERT: A 812 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6053 (ptm) REVERT: A 907 PHE cc_start: 0.7939 (t80) cc_final: 0.7152 (t80) REVERT: A 1128 ARG cc_start: 0.5850 (mmm160) cc_final: 0.5398 (mmt-90) REVERT: B 74 GLN cc_start: 0.7614 (mp10) cc_final: 0.7247 (mp10) REVERT: C 197 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7416 (tt) REVERT: C 256 LEU cc_start: 0.7966 (tt) cc_final: 0.7630 (tp) REVERT: C 400 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7312 (tm-30) REVERT: C 479 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6420 (pt) outliers start: 42 outliers final: 29 residues processed: 234 average time/residue: 0.2739 time to fit residues: 95.4154 Evaluate side-chains 230 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 130 LEU 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 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 593 SER 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 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 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU 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 197 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 145 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS B 409 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN C 187 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14702 Z= 0.302 Angle : 0.731 13.010 20090 Z= 0.368 Chirality : 0.045 0.295 2184 Planarity : 0.005 0.049 2452 Dihedral : 17.110 175.107 2231 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.93 % Favored : 90.89 % Rotamer: Outliers : 3.05 % Allowed : 20.96 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1680 helix: 0.32 (0.22), residues: 603 sheet: -0.89 (0.34), residues: 221 loop : -1.97 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 312 HIS 0.014 0.001 HIS C 258 PHE 0.015 0.002 PHE A 610 TYR 0.019 0.002 TYR A 434 ARG 0.006 0.001 ARG A 869 *********************** 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 245 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.6465 (tpt-90) cc_final: 0.5230 (ttt-90) REVERT: A 299 MET cc_start: 0.6470 (mmp) cc_final: 0.6124 (mmm) REVERT: A 345 TRP cc_start: 0.5189 (m-90) cc_final: 0.3601 (t-100) REVERT: A 356 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2987 (tt) REVERT: A 812 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6123 (ptm) REVERT: A 907 PHE cc_start: 0.8070 (t80) cc_final: 0.7295 (t80) REVERT: A 1128 ARG cc_start: 0.5991 (mmm160) cc_final: 0.5504 (mmt-90) REVERT: A 1214 GLN cc_start: 0.6706 (tm-30) cc_final: 0.6377 (tm-30) REVERT: C 256 LEU cc_start: 0.8138 (tt) cc_final: 0.7836 (tp) REVERT: C 400 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7362 (tm-30) REVERT: C 479 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6572 (pt) outliers start: 44 outliers final: 29 residues processed: 233 average time/residue: 0.2621 time to fit residues: 90.8119 Evaluate side-chains 228 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 130 LEU 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 356 LEU Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU 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 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 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 70 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 77 optimal weight: 0.0070 chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 HIS B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.3725 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= 0.190 Angle : 0.701 12.300 20090 Z= 0.349 Chirality : 0.043 0.221 2184 Planarity : 0.004 0.049 2452 Dihedral : 17.032 175.072 2231 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.21 % Favored : 91.61 % Rotamer: Outliers : 2.36 % Allowed : 22.21 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1680 helix: 0.52 (0.22), residues: 596 sheet: -0.68 (0.33), residues: 215 loop : -1.89 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 312 HIS 0.011 0.001 HIS C 258 PHE 0.023 0.001 PHE A 961 TYR 0.014 0.001 TYR A 434 ARG 0.007 0.000 ARG B 325 ********************** 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 234 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.4801 (t80) cc_final: 0.4492 (t80) REVERT: A 812 MET cc_start: 0.7002 (ppp) cc_final: 0.6106 (ptm) REVERT: A 907 PHE cc_start: 0.8000 (t80) cc_final: 0.7311 (t80) REVERT: A 1128 ARG cc_start: 0.5752 (mmm160) cc_final: 0.5476 (mtt-85) REVERT: A 1214 GLN cc_start: 0.6634 (tm-30) cc_final: 0.6363 (tm-30) REVERT: B 74 GLN cc_start: 0.7604 (mp10) cc_final: 0.7279 (mp10) REVERT: C 256 LEU cc_start: 0.8022 (tt) cc_final: 0.7686 (tp) REVERT: C 351 TYR cc_start: 0.7680 (m-80) cc_final: 0.7431 (m-80) REVERT: C 400 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7311 (tm-30) REVERT: C 479 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6376 (pt) outliers start: 34 outliers final: 28 residues processed: 226 average time/residue: 0.2689 time to fit residues: 90.0979 Evaluate side-chains 223 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 130 LEU 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 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU 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 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 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 70 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 HIS B 368 HIS B 409 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.183717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139450 restraints weight = 28470.278| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.16 r_work: 0.3707 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14702 Z= 0.240 Angle : 0.715 12.251 20090 Z= 0.358 Chirality : 0.044 0.232 2184 Planarity : 0.004 0.048 2452 Dihedral : 17.003 175.073 2231 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.51 % Favored : 91.31 % Rotamer: Outliers : 2.64 % Allowed : 22.35 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1680 helix: 0.41 (0.22), residues: 602 sheet: -0.71 (0.34), residues: 211 loop : -1.93 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 312 HIS 0.005 0.001 HIS B 77 PHE 0.021 0.002 PHE A 750 TYR 0.025 0.002 TYR B 432 ARG 0.006 0.000 ARG B 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.99 seconds wall clock time: 61 minutes 31.58 seconds (3691.58 seconds total)