Starting phenix.real_space_refine on Thu May 15 17:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekb_48117/05_2025/9ekb_48117.cif" } resolution = 3.65 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= 0.026 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 S 79 5.16 5 C 8442 2.51 5 N 2329 2.21 5 O 2469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8202 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 69, 'TRANS': 971} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1041, 8202 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 69, 'TRANS': 971} Chain breaks: 3 bond proxies already assigned to first conformer: 8370 Chain: "B" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3402 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 407} Chain breaks: 1 Chain: "C" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 582 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 7, 'TRANS': 61} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' ZN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7420 SG CYS A1012 17.424 57.992 52.643 1.00174.63 S ATOM 7438 SG CYS A1015 14.489 59.537 52.414 1.00181.12 S ATOM 7518 SG CYS A1026 14.746 58.407 49.494 1.00180.80 S ATOM 7544 SG CYS A1029 17.388 61.174 50.652 1.00175.46 S ATOM 7896 SG CYS A1071 39.209 41.890 85.962 1.00122.69 S ATOM 7934 SG CYS A1076 39.236 48.108 84.884 1.00148.70 S ATOM 7795 SG CYS A1058 40.166 43.768 80.594 1.00128.76 S ATOM 7821 SG CYS A1061 44.256 44.429 85.392 1.00132.37 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1100 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1100 " occ=0.50 Time building chain proxies: 11.92, per 1000 atoms: 0.89 Number of scatterers: 13324 At special positions: 0 Unit cell: (86.24, 113.12, 173.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 79 16.00 O 2469 8.00 N 2329 7.00 C 8442 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: 4.22 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3170 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 42.1% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.626A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.786A pdb=" N MET A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.593A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.248A pdb=" N ARG A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.640A pdb=" N TYR A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 490 through 499 removed outlier: 3.560A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 527 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 527 through 539 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.543A pdb=" N SER A 548 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.867A pdb=" N VAL A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.559A pdb=" N GLN A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 705 removed outlier: 4.335A pdb=" N TYR A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 739 removed outlier: 4.110A pdb=" N SER A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 767 through 784 Processing helix chain 'A' and resid 837 through 853 removed outlier: 3.960A pdb=" N ALA A 841 " --> pdb=" O CYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 873 Processing helix chain 'A' and resid 877 through 882 removed outlier: 3.736A pdb=" N VAL A 882 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 898 through 911 Processing helix chain 'A' and resid 934 through 937 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 953 through 962 removed outlier: 3.724A pdb=" N TYR A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 977 through 985 Processing helix chain 'A' and resid 1029 through 1031 No H-bonds generated for 'chain 'A' and resid 1029 through 1031' Processing helix chain 'A' and resid 1032 through 1063 removed outlier: 3.739A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A1055 " --> pdb=" O PHE A1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1097 removed outlier: 4.039A pdb=" N TYR A1080 " --> pdb=" O CYS A1076 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.582A pdb=" N TYR B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.554A pdb=" N GLU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 208 through 223 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.729A pdb=" N GLN B 253 " --> pdb=" O HIS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 288 removed outlier: 4.017A pdb=" N ALA B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 22 through 31 removed outlier: 3.758A pdb=" N LEU C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 52 removed outlier: 3.794A pdb=" N ARG C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 126 through 129 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 81 through 91 removed outlier: 3.949A pdb=" N TRP D 85 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.593A pdb=" N LEU A 286 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 142 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 122 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 105 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 124 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N HIS A 103 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG A 126 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 101 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE A 128 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 removed outlier: 7.979A pdb=" N LEU A 569 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 196 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 371 removed outlier: 3.669A pdb=" N GLN A 369 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 371 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 335 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY A 395 " --> pdb=" O MET A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.987A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 600 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 797 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 598 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET A 760 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.987A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AA8, first strand: chain 'A' and resid 883 through 886 Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 25 removed outlier: 6.808A pdb=" N PHE B 24 " --> pdb=" O GLN C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.726A pdb=" N ARG B 340 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE B 403 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 342 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY B 405 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B 344 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N THR B 407 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 100 removed outlier: 5.248A pdb=" N LEU B 133 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR B 176 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA B 160 " --> pdb=" O TYR B 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 327 removed outlier: 8.739A pdb=" N ASP B 293 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 241 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET B 295 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 243 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE B 195 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 241 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 197 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU B 243 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 199 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER C 73 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 79 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU C 62 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL C 100 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER C 64 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE C 98 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N SER C 66 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA C 96 " --> pdb=" O SER C 66 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 5690 1.44 - 1.65: 7812 1.65 - 1.86: 107 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 13621 Sorted by residual: bond pdb=" C SER A 788 " pdb=" N PRO A 789 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.20e+00 bond pdb=" CA VAL A 596 " pdb=" CB VAL A 596 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 1.07e+00 bond pdb=" C ASN B 330 " pdb=" O ASN B 330 " ideal model delta sigma weight residual 1.244 1.236 0.008 9.10e-03 1.21e+04 8.08e-01 bond pdb=" CA PHE A 799 " pdb=" C PHE A 799 " ideal model delta sigma weight residual 1.521 1.531 -0.009 1.08e-02 8.57e+03 7.63e-01 bond pdb=" N ASN B 330 " pdb=" CA ASN B 330 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.54e-01 ... (remaining 13616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 18047 1.21 - 2.43: 324 2.43 - 3.64: 103 3.64 - 4.86: 11 4.86 - 6.07: 8 Bond angle restraints: 18493 Sorted by residual: angle pdb=" N PRO A 789 " pdb=" CA PRO A 789 " pdb=" C PRO A 789 " ideal model delta sigma weight residual 112.47 118.35 -5.88 2.06e+00 2.36e-01 8.15e+00 angle pdb=" N LYS A 738 " pdb=" CA LYS A 738 " pdb=" C LYS A 738 " ideal model delta sigma weight residual 111.03 113.66 -2.63 1.11e+00 8.12e-01 5.59e+00 angle pdb=" C TYR C 101 " pdb=" N SER C 102 " pdb=" CA SER C 102 " ideal model delta sigma weight residual 122.37 118.59 3.78 1.72e+00 3.38e-01 4.83e+00 angle pdb=" C THR B 305 " pdb=" N LEU B 306 " pdb=" CA LEU B 306 " ideal model delta sigma weight residual 121.80 116.56 5.24 2.44e+00 1.68e-01 4.61e+00 angle pdb=" C LEU B 327 " pdb=" N VAL B 328 " pdb=" CA VAL B 328 " ideal model delta sigma weight residual 122.92 119.92 3.00 1.44e+00 4.82e-01 4.33e+00 ... (remaining 18488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 7864 15.91 - 31.82: 360 31.82 - 47.74: 63 47.74 - 63.65: 9 63.65 - 79.56: 2 Dihedral angle restraints: 8298 sinusoidal: 3386 harmonic: 4912 Sorted by residual: dihedral pdb=" CA ALA B 244 " pdb=" C ALA B 244 " pdb=" N GLY B 245 " pdb=" CA GLY B 245 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 dihedral pdb=" N GLU B 132 " pdb=" CA GLU B 132 " pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " ideal model delta sinusoidal sigma weight residual -180.00 -120.25 -59.75 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 574 " pdb=" CB LYS A 574 " pdb=" CG LYS A 574 " pdb=" CD LYS A 574 " ideal model delta sinusoidal sigma weight residual -60.00 -119.24 59.24 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1438 0.036 - 0.072: 453 0.072 - 0.108: 132 0.108 - 0.144: 45 0.144 - 0.180: 1 Chirality restraints: 2069 Sorted by residual: chirality pdb=" CA PRO A 789 " pdb=" N PRO A 789 " pdb=" C PRO A 789 " pdb=" CB PRO A 789 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA ILE C 103 " pdb=" N ILE C 103 " pdb=" C ILE C 103 " pdb=" CB ILE C 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 334 " pdb=" N VAL A 334 " pdb=" C VAL A 334 " pdb=" CB VAL A 334 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2066 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 128 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 129 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 788 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 789 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 789 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 789 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 112 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO C 113 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " -0.019 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1243 2.74 - 3.28: 12554 3.28 - 3.82: 20367 3.82 - 4.36: 23043 4.36 - 4.90: 41225 Nonbonded interactions: 98432 Sorted by model distance: nonbonded pdb=" OG SER A1073 " pdb=" OD1 ASP A1075 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 593 " pdb=" O LEU A 851 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 798 " pdb=" OD2 ASP A 825 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 815 " pdb=" OD2 ASP A 822 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 200 " pdb=" OD1 ASN B 406 " model vdw 2.256 3.040 ... (remaining 98427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.270 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.930 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 0.341 13629 Z= 0.166 Angle : 1.018 52.960 18511 Z= 0.260 Chirality : 0.041 0.180 2069 Planarity : 0.004 0.037 2415 Dihedral : 9.437 79.561 5128 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 1.91 % Allowed : 4.03 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.07 (0.21), residues: 1681 helix: 1.89 (0.22), residues: 610 sheet: 0.81 (0.33), residues: 253 loop : -0.19 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 344 HIS 0.002 0.001 HIS A 988 PHE 0.008 0.001 PHE A 96 TYR 0.013 0.001 TYR C 61 ARG 0.002 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.15160 ( 596) hydrogen bonds : angle 6.36490 ( 1680) metal coordination : bond 0.16962 ( 8) metal coordination : angle 29.01403 ( 18) covalent geometry : bond 0.00255 (13621) covalent geometry : angle 0.46770 (18493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7469 (ttm) cc_final: 0.7239 (ttp) REVERT: A 59 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: A 448 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7476 (m) REVERT: A 466 GLU cc_start: 0.6103 (mt-10) cc_final: 0.5851 (tt0) REVERT: A 564 MET cc_start: 0.8410 (ttp) cc_final: 0.7901 (mmt) REVERT: A 612 MET cc_start: 0.6459 (mtm) cc_final: 0.6203 (mtp) REVERT: A 620 THR cc_start: 0.8430 (p) cc_final: 0.8180 (t) REVERT: A 635 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7152 (t0) REVERT: A 725 ARG cc_start: 0.5905 (mtm-85) cc_final: 0.5693 (mtt180) REVERT: A 905 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8827 (mt-10) REVERT: A 988 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7311 (p-80) REVERT: B 61 MET cc_start: 0.8153 (mmm) cc_final: 0.7462 (mtt) REVERT: B 304 TYR cc_start: 0.8791 (t80) cc_final: 0.8555 (t80) REVERT: B 358 MET cc_start: 0.9219 (mtm) cc_final: 0.8954 (mtm) REVERT: B 380 ASP cc_start: 0.8872 (t70) cc_final: 0.8529 (t0) REVERT: C 46 GLU cc_start: 0.5583 (mm-30) cc_final: 0.5310 (mm-30) REVERT: C 70 ASN cc_start: 0.8071 (m-40) cc_final: 0.7402 (p0) REVERT: D 89 LYS cc_start: 0.8450 (tttt) cc_final: 0.8184 (ttmt) REVERT: D 95 PRO cc_start: 0.8533 (Cg_endo) cc_final: 0.8126 (Cg_exo) REVERT: D 101 LEU cc_start: 0.9062 (tp) cc_final: 0.8684 (tp) outliers start: 28 outliers final: 7 residues processed: 248 average time/residue: 0.3062 time to fit residues: 103.8283 Evaluate side-chains 116 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 988 HIS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 59 GLN A 142 HIS A 204 HIS A 298 HIS A 305 GLN A 437 GLN B 120 GLN B 250 HIS B 303 ASN B 326 GLN B 347 GLN B 361 HIS C 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091680 restraints weight = 25324.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093600 restraints weight = 15990.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094239 restraints weight = 11156.845| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13629 Z= 0.157 Angle : 0.730 25.821 18511 Z= 0.302 Chirality : 0.043 0.192 2069 Planarity : 0.005 0.045 2415 Dihedral : 4.681 48.233 1878 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Rotamer: Outliers : 2.32 % Allowed : 8.82 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.27 (0.21), residues: 1681 helix: 2.28 (0.22), residues: 621 sheet: 0.81 (0.33), residues: 254 loop : -0.27 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 102 HIS 0.003 0.001 HIS A 614 PHE 0.011 0.001 PHE A 814 TYR 0.014 0.001 TYR B 385 ARG 0.008 0.001 ARG A 849 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 596) hydrogen bonds : angle 4.88899 ( 1680) metal coordination : bond 0.00967 ( 8) metal coordination : angle 13.81339 ( 18) covalent geometry : bond 0.00368 (13621) covalent geometry : angle 0.59024 (18493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8316 (mtp) cc_final: 0.7886 (mtt) REVERT: A 245 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7891 (pt0) REVERT: A 315 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8628 (p90) REVERT: A 388 MET cc_start: 0.8164 (tmm) cc_final: 0.7551 (tmm) REVERT: A 448 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7728 (m) REVERT: A 466 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5951 (tt0) REVERT: A 564 MET cc_start: 0.8423 (ttp) cc_final: 0.7979 (mmt) REVERT: A 620 THR cc_start: 0.8422 (p) cc_final: 0.8096 (t) REVERT: A 725 ARG cc_start: 0.6191 (mtm-85) cc_final: 0.5890 (mtt180) REVERT: A 827 LYS cc_start: 0.8298 (tppp) cc_final: 0.7883 (ttpt) REVERT: A 905 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8878 (mt-10) REVERT: A 940 GLU cc_start: 0.7908 (tp30) cc_final: 0.7499 (mm-30) REVERT: A 988 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7443 (p-80) REVERT: B 358 MET cc_start: 0.9180 (mtm) cc_final: 0.8969 (mtm) REVERT: B 380 ASP cc_start: 0.8863 (t70) cc_final: 0.8475 (t0) REVERT: C 3 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5237 (t0) REVERT: C 46 GLU cc_start: 0.5762 (mm-30) cc_final: 0.5504 (mm-30) REVERT: C 70 ASN cc_start: 0.8023 (m-40) cc_final: 0.7459 (p0) REVERT: C 128 ASN cc_start: 0.7906 (m-40) cc_final: 0.6581 (p0) REVERT: D 89 LYS cc_start: 0.8639 (tttt) cc_final: 0.8414 (ttmt) REVERT: D 95 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.8049 (Cg_exo) outliers start: 34 outliers final: 18 residues processed: 142 average time/residue: 0.2442 time to fit residues: 51.8378 Evaluate side-chains 124 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 988 HIS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090295 restraints weight = 25157.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093832 restraints weight = 14270.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096820 restraints weight = 9008.713| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13629 Z= 0.137 Angle : 0.577 12.268 18511 Z= 0.278 Chirality : 0.042 0.228 2069 Planarity : 0.004 0.056 2415 Dihedral : 4.321 46.823 1869 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 2.32 % Allowed : 9.16 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.31 (0.21), residues: 1681 helix: 2.37 (0.22), residues: 621 sheet: 0.82 (0.34), residues: 249 loop : -0.28 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 102 HIS 0.013 0.001 HIS B 250 PHE 0.009 0.001 PHE A 96 TYR 0.013 0.001 TYR C 6 ARG 0.004 0.000 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 596) hydrogen bonds : angle 4.61190 ( 1680) metal coordination : bond 0.00739 ( 8) metal coordination : angle 6.05141 ( 18) covalent geometry : bond 0.00320 (13621) covalent geometry : angle 0.54588 (18493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8298 (mtp) cc_final: 0.7872 (mtt) REVERT: A 245 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7796 (pt0) REVERT: A 315 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8579 (p90) REVERT: A 388 MET cc_start: 0.8123 (tmm) cc_final: 0.7426 (tmm) REVERT: A 466 GLU cc_start: 0.6197 (mt-10) cc_final: 0.5954 (tt0) REVERT: A 564 MET cc_start: 0.8289 (ttp) cc_final: 0.7872 (mmt) REVERT: A 620 THR cc_start: 0.8387 (p) cc_final: 0.8073 (t) REVERT: A 725 ARG cc_start: 0.6106 (mtm-85) cc_final: 0.5821 (mtt180) REVERT: A 905 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8873 (mt-10) REVERT: A 937 MET cc_start: 0.8216 (tpp) cc_final: 0.7672 (tpp) REVERT: B 312 HIS cc_start: 0.7849 (t-90) cc_final: 0.7428 (t-90) REVERT: B 358 MET cc_start: 0.9152 (mtm) cc_final: 0.8933 (mtm) REVERT: B 380 ASP cc_start: 0.8890 (t70) cc_final: 0.8492 (t0) REVERT: C 3 ASP cc_start: 0.5791 (OUTLIER) cc_final: 0.4978 (t0) REVERT: C 46 GLU cc_start: 0.5693 (mm-30) cc_final: 0.5428 (mm-30) REVERT: C 70 ASN cc_start: 0.8020 (m-40) cc_final: 0.7425 (p0) REVERT: C 128 ASN cc_start: 0.7897 (m-40) cc_final: 0.6586 (p0) REVERT: D 89 LYS cc_start: 0.8583 (tttt) cc_final: 0.8303 (ttmt) outliers start: 34 outliers final: 21 residues processed: 129 average time/residue: 0.2442 time to fit residues: 47.2326 Evaluate side-chains 123 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 166 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 0.0060 chunk 150 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN B 250 HIS ** C 52 ASN ** 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 = 0.3767 r_free = 0.3767 target = 0.123790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091923 restraints weight = 25179.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.095980 restraints weight = 14551.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.097687 restraints weight = 9037.818| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13629 Z= 0.104 Angle : 0.515 8.527 18511 Z= 0.254 Chirality : 0.041 0.213 2069 Planarity : 0.004 0.057 2415 Dihedral : 4.011 46.379 1862 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.84 % Rotamer: Outliers : 2.32 % Allowed : 9.64 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.48 (0.22), residues: 1681 helix: 2.51 (0.22), residues: 623 sheet: 0.95 (0.34), residues: 241 loop : -0.20 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 102 HIS 0.004 0.001 HIS A 988 PHE 0.015 0.001 PHE A 350 TYR 0.014 0.001 TYR A 511 ARG 0.005 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 596) hydrogen bonds : angle 4.37487 ( 1680) metal coordination : bond 0.00483 ( 8) metal coordination : angle 3.53324 ( 18) covalent geometry : bond 0.00233 (13621) covalent geometry : angle 0.50336 (18493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8258 (mtp) cc_final: 0.7823 (mtt) REVERT: A 315 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8510 (p90) REVERT: A 388 MET cc_start: 0.8084 (tmm) cc_final: 0.7244 (tmm) REVERT: A 466 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5927 (tt0) REVERT: A 487 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: A 514 LYS cc_start: 0.5406 (mmtt) cc_final: 0.5075 (mptt) REVERT: A 564 MET cc_start: 0.8383 (ttp) cc_final: 0.7831 (mmt) REVERT: A 620 THR cc_start: 0.8341 (p) cc_final: 0.8043 (t) REVERT: A 725 ARG cc_start: 0.6077 (mtm-85) cc_final: 0.5774 (mtt180) REVERT: A 905 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8842 (mt-10) REVERT: A 937 MET cc_start: 0.8045 (tpp) cc_final: 0.7555 (tpp) REVERT: B 312 HIS cc_start: 0.7759 (t-90) cc_final: 0.7425 (t-90) REVERT: B 380 ASP cc_start: 0.8865 (t70) cc_final: 0.8464 (t0) REVERT: C 3 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.4954 (t0) REVERT: C 46 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5314 (mm-30) REVERT: C 128 ASN cc_start: 0.7815 (m-40) cc_final: 0.6475 (p0) REVERT: D 89 LYS cc_start: 0.8627 (tttt) cc_final: 0.8380 (ttmt) outliers start: 34 outliers final: 24 residues processed: 129 average time/residue: 0.2394 time to fit residues: 46.9214 Evaluate side-chains 122 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN B 250 HIS ** C 52 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.123995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091872 restraints weight = 25294.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096379 restraints weight = 14783.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.097962 restraints weight = 9212.060| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13629 Z= 0.105 Angle : 0.511 7.542 18511 Z= 0.252 Chirality : 0.041 0.205 2069 Planarity : 0.004 0.060 2415 Dihedral : 3.950 45.094 1862 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 2.19 % Allowed : 9.91 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.51 (0.22), residues: 1681 helix: 2.53 (0.22), residues: 625 sheet: 0.83 (0.33), residues: 250 loop : -0.15 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 102 HIS 0.015 0.001 HIS A 988 PHE 0.017 0.001 PHE A 350 TYR 0.011 0.001 TYR C 6 ARG 0.004 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 596) hydrogen bonds : angle 4.29649 ( 1680) metal coordination : bond 0.00449 ( 8) metal coordination : angle 3.35839 ( 18) covalent geometry : bond 0.00238 (13621) covalent geometry : angle 0.49996 (18493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6595 (ttm) cc_final: 0.6048 (tmm) REVERT: A 44 MET cc_start: 0.8145 (mtp) cc_final: 0.7694 (mtt) REVERT: A 315 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8496 (p90) REVERT: A 388 MET cc_start: 0.8066 (tmm) cc_final: 0.6799 (tmm) REVERT: A 466 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5927 (tt0) REVERT: A 514 LYS cc_start: 0.5397 (mmtt) cc_final: 0.4968 (mptt) REVERT: A 564 MET cc_start: 0.8363 (ttp) cc_final: 0.7824 (mmt) REVERT: A 620 THR cc_start: 0.8335 (p) cc_final: 0.8031 (t) REVERT: A 725 ARG cc_start: 0.6025 (mtm-85) cc_final: 0.5722 (mtt180) REVERT: A 905 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8823 (mt-10) REVERT: A 937 MET cc_start: 0.8086 (tpp) cc_final: 0.7604 (tpp) REVERT: B 312 HIS cc_start: 0.7782 (t-90) cc_final: 0.7435 (t-90) REVERT: B 380 ASP cc_start: 0.8866 (t70) cc_final: 0.8468 (t0) REVERT: C 3 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.4936 (t0) REVERT: C 46 GLU cc_start: 0.5687 (mm-30) cc_final: 0.5393 (mm-30) REVERT: C 128 ASN cc_start: 0.7781 (m-40) cc_final: 0.6451 (p0) REVERT: D 89 LYS cc_start: 0.8528 (tttt) cc_final: 0.8245 (ttmt) outliers start: 32 outliers final: 26 residues processed: 116 average time/residue: 0.2360 time to fit residues: 41.3959 Evaluate side-chains 120 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 0.0170 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS ** C 52 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092416 restraints weight = 25183.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096606 restraints weight = 14477.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098233 restraints weight = 8776.141| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13629 Z= 0.107 Angle : 0.508 8.173 18511 Z= 0.250 Chirality : 0.041 0.201 2069 Planarity : 0.004 0.062 2415 Dihedral : 3.910 44.699 1862 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 9.84 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.58 (0.22), residues: 1681 helix: 2.54 (0.22), residues: 626 sheet: 0.91 (0.34), residues: 243 loop : -0.08 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 102 HIS 0.009 0.001 HIS A 988 PHE 0.017 0.001 PHE A 350 TYR 0.017 0.001 TYR A 149 ARG 0.004 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 596) hydrogen bonds : angle 4.28102 ( 1680) metal coordination : bond 0.00442 ( 8) metal coordination : angle 3.18773 ( 18) covalent geometry : bond 0.00247 (13621) covalent geometry : angle 0.49864 (18493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8149 (mtp) cc_final: 0.7718 (mtt) REVERT: A 149 TYR cc_start: 0.7615 (m-80) cc_final: 0.7386 (m-80) REVERT: A 315 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8494 (p90) REVERT: A 388 MET cc_start: 0.8054 (tmm) cc_final: 0.6822 (tmm) REVERT: A 466 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5926 (tt0) REVERT: A 487 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: A 564 MET cc_start: 0.8355 (ttp) cc_final: 0.7851 (mmt) REVERT: A 620 THR cc_start: 0.8326 (p) cc_final: 0.8021 (t) REVERT: A 725 ARG cc_start: 0.6034 (mtm-85) cc_final: 0.5726 (mtt180) REVERT: A 877 ASP cc_start: 0.7730 (t0) cc_final: 0.7313 (t0) REVERT: A 905 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8837 (mt-10) REVERT: A 937 MET cc_start: 0.8122 (tpp) cc_final: 0.7607 (tpp) REVERT: B 312 HIS cc_start: 0.7777 (t-90) cc_final: 0.7358 (t-90) REVERT: B 380 ASP cc_start: 0.8866 (t70) cc_final: 0.8469 (t0) REVERT: C 3 ASP cc_start: 0.5932 (OUTLIER) cc_final: 0.5430 (t0) REVERT: C 46 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5384 (mm-30) REVERT: D 89 LYS cc_start: 0.8506 (tttt) cc_final: 0.8212 (ttmt) outliers start: 36 outliers final: 28 residues processed: 121 average time/residue: 0.2410 time to fit residues: 43.7604 Evaluate side-chains 120 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 0.0060 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 326 GLN ** C 52 ASN ** 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 = 0.3717 r_free = 0.3717 target = 0.119980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.088236 restraints weight = 26068.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091857 restraints weight = 15950.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093485 restraints weight = 10302.340| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13629 Z= 0.211 Angle : 0.602 7.316 18511 Z= 0.302 Chirality : 0.044 0.212 2069 Planarity : 0.005 0.058 2415 Dihedral : 4.222 44.669 1862 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 2.32 % Allowed : 10.46 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.24 (0.22), residues: 1681 helix: 2.27 (0.21), residues: 625 sheet: 0.63 (0.33), residues: 251 loop : -0.25 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 25 HIS 0.023 0.001 HIS B 250 PHE 0.018 0.002 PHE A 350 TYR 0.020 0.002 TYR B 385 ARG 0.003 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 596) hydrogen bonds : angle 4.59017 ( 1680) metal coordination : bond 0.00761 ( 8) metal coordination : angle 3.25167 ( 18) covalent geometry : bond 0.00511 (13621) covalent geometry : angle 0.59418 (18493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8234 (mtp) cc_final: 0.7793 (mtt) REVERT: A 315 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8618 (p90) REVERT: A 466 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6002 (tt0) REVERT: A 487 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: A 514 LYS cc_start: 0.5207 (mptt) cc_final: 0.4951 (mmtt) REVERT: A 564 MET cc_start: 0.8240 (ttp) cc_final: 0.7889 (mmt) REVERT: A 620 THR cc_start: 0.8436 (p) cc_final: 0.8106 (t) REVERT: A 725 ARG cc_start: 0.6126 (mtm-85) cc_final: 0.5780 (mtt180) REVERT: A 905 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8849 (mt-10) REVERT: A 937 MET cc_start: 0.8322 (tpp) cc_final: 0.7818 (tpp) REVERT: B 312 HIS cc_start: 0.7946 (t-90) cc_final: 0.7470 (t-90) REVERT: B 380 ASP cc_start: 0.8909 (t70) cc_final: 0.8476 (t0) REVERT: C 3 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5421 (t0) REVERT: C 46 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5657 (mm-30) REVERT: D 89 LYS cc_start: 0.8823 (tttt) cc_final: 0.8602 (ttmt) outliers start: 34 outliers final: 27 residues processed: 113 average time/residue: 0.2540 time to fit residues: 43.0947 Evaluate side-chains 118 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain B residue 11 HIS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 326 GLN ** C 52 ASN ** 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 = 0.3755 r_free = 0.3755 target = 0.122773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090843 restraints weight = 25269.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095398 restraints weight = 14453.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097275 restraints weight = 8544.627| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13629 Z= 0.114 Angle : 0.525 7.258 18511 Z= 0.259 Chirality : 0.042 0.203 2069 Planarity : 0.004 0.060 2415 Dihedral : 4.046 44.865 1862 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 1.78 % Allowed : 11.07 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.39 (0.22), residues: 1681 helix: 2.43 (0.21), residues: 625 sheet: 0.63 (0.33), residues: 252 loop : -0.17 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 102 HIS 0.008 0.001 HIS A 988 PHE 0.017 0.001 PHE A 350 TYR 0.017 0.001 TYR A 511 ARG 0.003 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 596) hydrogen bonds : angle 4.38487 ( 1680) metal coordination : bond 0.00511 ( 8) metal coordination : angle 3.29636 ( 18) covalent geometry : bond 0.00263 (13621) covalent geometry : angle 0.51553 (18493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.5883 (ttp) cc_final: 0.5671 (tmm) REVERT: A 44 MET cc_start: 0.8207 (mtp) cc_final: 0.7750 (mtt) REVERT: A 315 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8507 (p90) REVERT: A 388 MET cc_start: 0.8155 (tmm) cc_final: 0.7624 (tmm) REVERT: A 466 GLU cc_start: 0.6359 (mt-10) cc_final: 0.5992 (tt0) REVERT: A 487 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: A 514 LYS cc_start: 0.5207 (mptt) cc_final: 0.4933 (mmtt) REVERT: A 564 MET cc_start: 0.8232 (ttp) cc_final: 0.7729 (mmt) REVERT: A 620 THR cc_start: 0.8357 (p) cc_final: 0.8046 (t) REVERT: A 725 ARG cc_start: 0.6090 (mtm-85) cc_final: 0.5748 (mtt180) REVERT: A 877 ASP cc_start: 0.7515 (t0) cc_final: 0.7266 (t0) REVERT: A 905 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8868 (mt-10) REVERT: A 937 MET cc_start: 0.8314 (tpp) cc_final: 0.7811 (tpp) REVERT: A 1081 MET cc_start: 0.7820 (mmm) cc_final: 0.7598 (mmm) REVERT: B 312 HIS cc_start: 0.7821 (t-90) cc_final: 0.7376 (t-90) REVERT: B 380 ASP cc_start: 0.8875 (t70) cc_final: 0.8484 (t0) REVERT: C 3 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5616 (t0) REVERT: C 46 GLU cc_start: 0.5742 (mm-30) cc_final: 0.5459 (mm-30) REVERT: D 89 LYS cc_start: 0.8594 (tttt) cc_final: 0.8330 (ttmm) outliers start: 26 outliers final: 22 residues processed: 111 average time/residue: 0.2449 time to fit residues: 41.5129 Evaluate side-chains 115 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 145 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** C 52 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.124364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093169 restraints weight = 24879.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097035 restraints weight = 13744.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098651 restraints weight = 8729.261| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13629 Z= 0.100 Angle : 0.510 7.343 18511 Z= 0.249 Chirality : 0.041 0.194 2069 Planarity : 0.004 0.064 2415 Dihedral : 3.894 44.349 1862 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 1.85 % Allowed : 11.07 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.52 (0.22), residues: 1681 helix: 2.53 (0.22), residues: 626 sheet: 0.81 (0.34), residues: 241 loop : -0.11 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 102 HIS 0.009 0.001 HIS B 250 PHE 0.016 0.001 PHE A 350 TYR 0.012 0.001 TYR C 61 ARG 0.004 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 596) hydrogen bonds : angle 4.24480 ( 1680) metal coordination : bond 0.00416 ( 8) metal coordination : angle 3.28281 ( 18) covalent geometry : bond 0.00227 (13621) covalent geometry : angle 0.49939 (18493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.5742 (ttp) cc_final: 0.5467 (tmm) REVERT: A 44 MET cc_start: 0.8200 (mtp) cc_final: 0.7955 (mtp) REVERT: A 315 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8492 (p90) REVERT: A 388 MET cc_start: 0.8143 (tmm) cc_final: 0.7573 (tmm) REVERT: A 466 GLU cc_start: 0.6353 (mt-10) cc_final: 0.5993 (tt0) REVERT: A 487 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: A 514 LYS cc_start: 0.5165 (mptt) cc_final: 0.4964 (mmtt) REVERT: A 564 MET cc_start: 0.8278 (ttp) cc_final: 0.7787 (mmt) REVERT: A 620 THR cc_start: 0.8315 (p) cc_final: 0.8021 (t) REVERT: A 877 ASP cc_start: 0.7543 (t0) cc_final: 0.7236 (t0) REVERT: A 905 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8860 (mt-10) REVERT: A 937 MET cc_start: 0.8276 (tpp) cc_final: 0.7770 (tpp) REVERT: B 380 ASP cc_start: 0.8861 (t70) cc_final: 0.8476 (t0) REVERT: C 3 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5635 (t0) REVERT: C 46 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5409 (mm-30) REVERT: D 89 LYS cc_start: 0.8677 (tttt) cc_final: 0.8421 (ttmm) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 0.2762 time to fit residues: 46.8993 Evaluate side-chains 111 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 11 HIS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 114 optimal weight: 0.1980 chunk 86 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 122 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** C 52 ASN ** 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 = 0.3792 r_free = 0.3792 target = 0.125536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.094156 restraints weight = 24900.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098183 restraints weight = 14472.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100024 restraints weight = 9035.996| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13629 Z= 0.092 Angle : 0.503 7.442 18511 Z= 0.245 Chirality : 0.041 0.190 2069 Planarity : 0.004 0.070 2415 Dihedral : 3.810 44.087 1862 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 11.28 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.56 (0.22), residues: 1681 helix: 2.57 (0.21), residues: 625 sheet: 0.82 (0.34), residues: 243 loop : -0.09 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 102 HIS 0.008 0.001 HIS B 250 PHE 0.015 0.001 PHE A 350 TYR 0.018 0.001 TYR A 511 ARG 0.015 0.000 ARG A 725 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 596) hydrogen bonds : angle 4.15003 ( 1680) metal coordination : bond 0.00375 ( 8) metal coordination : angle 3.10465 ( 18) covalent geometry : bond 0.00203 (13621) covalent geometry : angle 0.49417 (18493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.469 Fit side-chains REVERT: A 44 MET cc_start: 0.8087 (mtp) cc_final: 0.7653 (mtm) REVERT: A 315 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8522 (p90) REVERT: A 385 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7287 (tp) REVERT: A 466 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6026 (tt0) REVERT: A 487 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: A 514 LYS cc_start: 0.5227 (mptt) cc_final: 0.4892 (mmtt) REVERT: A 564 MET cc_start: 0.8284 (ttp) cc_final: 0.7942 (mmt) REVERT: A 620 THR cc_start: 0.8322 (p) cc_final: 0.8015 (t) REVERT: A 725 ARG cc_start: 0.6632 (mtt180) cc_final: 0.6389 (mtt90) REVERT: A 877 ASP cc_start: 0.7405 (t0) cc_final: 0.6994 (t0) REVERT: A 905 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8883 (mt-10) REVERT: A 937 MET cc_start: 0.8271 (tpp) cc_final: 0.7760 (tpp) REVERT: A 1081 MET cc_start: 0.7674 (mmm) cc_final: 0.7424 (mmm) REVERT: B 380 ASP cc_start: 0.8793 (t70) cc_final: 0.8427 (t0) REVERT: C 3 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.5917 (t0) REVERT: C 46 GLU cc_start: 0.5679 (mm-30) cc_final: 0.5396 (mm-30) REVERT: D 89 LYS cc_start: 0.8732 (tttt) cc_final: 0.8489 (ttmm) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.2378 time to fit residues: 41.6746 Evaluate side-chains 108 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 11 HIS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 0.0570 chunk 133 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 250 HIS ** C 52 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.092768 restraints weight = 25065.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096935 restraints weight = 14162.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099131 restraints weight = 8639.012| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13629 Z= 0.105 Angle : 0.517 7.360 18511 Z= 0.251 Chirality : 0.041 0.189 2069 Planarity : 0.004 0.063 2415 Dihedral : 3.834 43.858 1862 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 1.64 % Allowed : 11.48 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.59 (0.22), residues: 1681 helix: 2.58 (0.21), residues: 626 sheet: 0.90 (0.34), residues: 241 loop : -0.09 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 102 HIS 0.008 0.001 HIS B 250 PHE 0.015 0.001 PHE A 350 TYR 0.013 0.001 TYR C 6 ARG 0.012 0.000 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 596) hydrogen bonds : angle 4.19620 ( 1680) metal coordination : bond 0.00429 ( 8) metal coordination : angle 3.25707 ( 18) covalent geometry : bond 0.00241 (13621) covalent geometry : angle 0.50724 (18493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4269.75 seconds wall clock time: 76 minutes 18.61 seconds (4578.61 seconds total)