Starting phenix.real_space_refine on Mon Dec 30 04:06:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.map" model { file = "/net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajn_15485/12_2024/8ajn_15485.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7603 2.51 5 N 2048 2.21 5 O 2298 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-5532/modules/chem_data/mon_lib" Total number of atoms: 12009 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8918 Classifications: {'peptide': 1140} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 1098} Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3091 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Time building chain proxies: 7.76, per 1000 atoms: 0.65 Number of scatterers: 12009 At special positions: 0 Unit cell: (92.105, 111.54, 147.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2298 8.00 N 2048 7.00 C 7603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 32 sheets defined 9.2% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.786A pdb=" N SER A 772 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 773 " --> pdb=" O LEU A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 773' Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1062 removed outlier: 4.189A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1090 through 1097 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1125 through 1138 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.654A pdb=" N VAL B 331 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.341A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.195A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.110A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.560A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 5.789A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 192 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TRP A 207 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU A 194 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A 205 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 196 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 203 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 221 removed outlier: 4.251A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 232 " --> pdb=" O MET A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.829A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 299 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU A 288 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 297 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 316 removed outlier: 6.642A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.968A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 396 through 402 removed outlier: 5.552A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.896A pdb=" N GLY A 409 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 435 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 457 through 463 removed outlier: 3.566A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.594A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 538 through 542 removed outlier: 4.390A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 588 through 596 removed outlier: 4.714A pdb=" N HIS A 600 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 611 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS A 628 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR A 613 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 626 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 637 through 643 removed outlier: 9.147A pdb=" N THR A 647 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER A 661 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.469A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.469A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 784 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 811 through 820 removed outlier: 4.983A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.827A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 911 through 917 removed outlier: 6.236A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.641A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC6, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 83 removed outlier: 7.436A pdb=" N GLY B 438 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 421 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.575A pdb=" N GLN B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B 112 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.028A pdb=" N ILE B 167 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 174 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.552A pdb=" N SER B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 239 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 255 through 261 removed outlier: 3.872A pdb=" N TYR B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE B 276 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 290 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 278 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.595A pdb=" N LYS B 332 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 343 through 349 removed outlier: 6.646A pdb=" N GLY B 356 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 346 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 354 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 348 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 343 through 349 removed outlier: 6.646A pdb=" N GLY B 356 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 346 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 354 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 348 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1278 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: 6.37 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3456 1.33 - 1.45: 2058 1.45 - 1.57: 6648 1.57 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 12251 Sorted by residual: bond pdb=" N ALA B 191 " pdb=" CA ALA B 191 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.16e-02 7.43e+03 4.26e+00 bond pdb=" CA HIS B 351 " pdb=" C HIS B 351 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.80e-02 3.09e+03 4.22e+00 bond pdb=" C SER B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 1.332 1.356 -0.023 1.20e-02 6.94e+03 3.76e+00 bond pdb=" C ILE B 190 " pdb=" N ALA B 191 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.25e-02 6.40e+03 3.11e+00 bond pdb=" CB PHE A 771 " pdb=" CG PHE A 771 " ideal model delta sigma weight residual 1.502 1.543 -0.041 2.30e-02 1.89e+03 3.10e+00 ... (remaining 12246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 14938 1.51 - 3.02: 1435 3.02 - 4.53: 208 4.53 - 6.04: 26 6.04 - 7.55: 3 Bond angle restraints: 16610 Sorted by residual: angle pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " pdb=" CG TYR B 48 " ideal model delta sigma weight residual 113.90 121.27 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" N ASN A 36 " pdb=" CA ASN A 36 " pdb=" C ASN A 36 " ideal model delta sigma weight residual 111.37 118.09 -6.72 1.65e+00 3.67e-01 1.66e+01 angle pdb=" N GLU A 779 " pdb=" CA GLU A 779 " pdb=" C GLU A 779 " ideal model delta sigma weight residual 111.82 116.12 -4.30 1.16e+00 7.43e-01 1.38e+01 angle pdb=" N ASP A 542 " pdb=" CA ASP A 542 " pdb=" C ASP A 542 " ideal model delta sigma weight residual 108.99 114.40 -5.41 1.57e+00 4.06e-01 1.19e+01 angle pdb=" CA TYR B 168 " pdb=" CB TYR B 168 " pdb=" CG TYR B 168 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 ... (remaining 16605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6869 17.86 - 35.72: 379 35.72 - 53.58: 67 53.58 - 71.44: 24 71.44 - 89.30: 9 Dihedral angle restraints: 7348 sinusoidal: 2930 harmonic: 4418 Sorted by residual: dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N ASP B 323 " pdb=" CA ASP B 323 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLU A 779 " pdb=" C GLU A 779 " pdb=" N THR A 780 " pdb=" CA THR A 780 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO B 418 " pdb=" C PRO B 418 " pdb=" N ASN B 419 " pdb=" CA ASN B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 7345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1158 0.040 - 0.080: 476 0.080 - 0.120: 179 0.120 - 0.160: 60 0.160 - 0.200: 15 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA ILE A1089 " pdb=" N ILE A1089 " pdb=" C ILE A1089 " pdb=" CB ILE A1089 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR B 213 " pdb=" CA THR B 213 " pdb=" OG1 THR B 213 " pdb=" CG2 THR B 213 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA VAL A 167 " pdb=" N VAL A 167 " pdb=" C VAL A 167 " pdb=" CB VAL A 167 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 1885 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 210 " -0.054 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" CG TRP B 210 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 210 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 210 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 210 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 210 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 210 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 210 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 210 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 210 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 295 " -0.045 2.00e-02 2.50e+03 2.32e-02 1.07e+01 pdb=" CG TYR B 295 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 295 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 295 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 295 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 295 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 965 " -0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE A 965 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 965 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 965 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 965 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 965 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 965 " -0.024 2.00e-02 2.50e+03 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 3893 2.85 - 3.36: 10936 3.36 - 3.87: 21319 3.87 - 4.39: 24659 4.39 - 4.90: 41835 Nonbonded interactions: 102642 Sorted by model distance: nonbonded pdb=" O ARG A 134 " pdb=" NH1 ARG A 134 " model vdw 2.334 3.120 nonbonded pdb=" NZ LYS B 51 " pdb=" OE1 GLU B 54 " model vdw 2.338 3.120 nonbonded pdb=" N PHE A 382 " pdb=" OG SER A 720 " model vdw 2.406 3.120 nonbonded pdb=" OE2 GLU A 969 " pdb=" N ASN A 973 " model vdw 2.436 3.120 nonbonded pdb=" O LEU A1093 " pdb=" OG SER A1096 " model vdw 2.440 3.040 ... (remaining 102637 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=0.00 max=1.00 mean=0.85 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.760 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.640 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 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 : 0.006 0.058 12251 Z= 0.398 Angle : 0.940 7.553 16610 Z= 0.564 Chirality : 0.053 0.200 1888 Planarity : 0.008 0.117 2143 Dihedral : 12.629 89.298 4505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.60 % Allowed : 3.29 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.11 (0.20), residues: 1522 helix: -1.34 (0.40), residues: 110 sheet: -0.44 (0.20), residues: 626 loop : -0.81 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP B 210 HIS 0.010 0.002 HIS A 189 PHE 0.049 0.005 PHE A 851 TYR 0.045 0.006 TYR B 295 ARG 0.009 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8409 (m-30) cc_final: 0.8038 (p0) REVERT: A 218 MET cc_start: 0.5572 (mtp) cc_final: 0.5241 (mtp) REVERT: A 900 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7596 (mmt90) REVERT: A 969 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5650 (pp20) REVERT: A 1036 MET cc_start: 0.5883 (tmt) cc_final: 0.5494 (tmt) REVERT: A 1105 MET cc_start: 0.5906 (mtt) cc_final: 0.5572 (mtt) REVERT: B 197 MET cc_start: 0.3753 (mtm) cc_final: 0.3491 (tpp) REVERT: B 390 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8668 (tp30) outliers start: 8 outliers final: 4 residues processed: 234 average time/residue: 1.4540 time to fit residues: 367.9817 Evaluate side-chains 104 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 188 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 809 GLN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12251 Z= 0.298 Angle : 0.732 9.139 16610 Z= 0.388 Chirality : 0.050 0.172 1888 Planarity : 0.005 0.050 2143 Dihedral : 6.706 92.033 1662 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.84 % Allowed : 10.60 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.01 (0.20), residues: 1522 helix: -0.17 (0.48), residues: 110 sheet: -0.46 (0.19), residues: 666 loop : -0.83 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 210 HIS 0.011 0.001 HIS A 600 PHE 0.035 0.002 PHE A 851 TYR 0.018 0.002 TYR A 891 ARG 0.006 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.5564 (mtp) cc_final: 0.5320 (mtp) REVERT: A 786 VAL cc_start: 0.6945 (t) cc_final: 0.6597 (m) REVERT: A 900 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7586 (mmt90) outliers start: 38 outliers final: 8 residues processed: 149 average time/residue: 1.0426 time to fit residues: 173.0552 Evaluate side-chains 98 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12251 Z= 0.310 Angle : 0.709 9.815 16610 Z= 0.370 Chirality : 0.048 0.166 1888 Planarity : 0.005 0.045 2143 Dihedral : 5.735 23.440 1649 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.06 % Allowed : 13.07 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.01 (0.21), residues: 1522 helix: -0.22 (0.48), residues: 125 sheet: -0.38 (0.20), residues: 662 loop : -0.93 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 210 HIS 0.004 0.001 HIS A 22 PHE 0.032 0.002 PHE A 851 TYR 0.018 0.002 TYR A 891 ARG 0.005 0.001 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3871 (t0) cc_final: 0.3497 (t0) REVERT: A 218 MET cc_start: 0.5569 (mtp) cc_final: 0.5364 (mtp) REVERT: A 282 MET cc_start: 0.7705 (tpp) cc_final: 0.7480 (tpt) REVERT: A 839 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: A 900 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7607 (mpt90) REVERT: B 188 PHE cc_start: 0.6022 (m-10) cc_final: 0.5781 (m-10) outliers start: 41 outliers final: 12 residues processed: 127 average time/residue: 1.0286 time to fit residues: 146.0780 Evaluate side-chains 100 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12251 Z= 0.226 Angle : 0.664 10.152 16610 Z= 0.340 Chirality : 0.047 0.189 1888 Planarity : 0.004 0.042 2143 Dihedral : 5.417 22.249 1649 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.61 % Allowed : 14.26 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.09 (0.21), residues: 1522 helix: -0.08 (0.48), residues: 127 sheet: -0.49 (0.19), residues: 650 loop : -0.95 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.005 0.001 HIS A 905 PHE 0.025 0.002 PHE A 851 TYR 0.021 0.002 TYR A 678 ARG 0.003 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3569 (t0) cc_final: 0.3238 (t0) REVERT: A 171 TYR cc_start: 0.5929 (m-80) cc_final: 0.5679 (m-80) REVERT: A 839 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: A 877 ASN cc_start: 0.7884 (p0) cc_final: 0.7285 (p0) REVERT: A 900 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7568 (mpt90) outliers start: 35 outliers final: 13 residues processed: 123 average time/residue: 1.1360 time to fit residues: 154.2155 Evaluate side-chains 98 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 61 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 102 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 GLN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12251 Z= 0.279 Angle : 0.678 10.374 16610 Z= 0.352 Chirality : 0.048 0.181 1888 Planarity : 0.004 0.043 2143 Dihedral : 5.478 22.643 1649 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.76 % Allowed : 15.68 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.22 (0.21), residues: 1522 helix: -0.13 (0.47), residues: 126 sheet: -0.65 (0.19), residues: 659 loop : -0.97 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 210 HIS 0.006 0.001 HIS B 318 PHE 0.032 0.002 PHE A 67 TYR 0.018 0.002 TYR A 678 ARG 0.004 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3815 (t0) cc_final: 0.3563 (t0) REVERT: A 839 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: A 877 ASN cc_start: 0.7949 (p0) cc_final: 0.7413 (p0) REVERT: A 900 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7507 (mmt90) outliers start: 37 outliers final: 11 residues processed: 122 average time/residue: 1.0019 time to fit residues: 137.0407 Evaluate side-chains 93 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1074 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12251 Z= 0.369 Angle : 0.745 9.887 16610 Z= 0.385 Chirality : 0.049 0.172 1888 Planarity : 0.005 0.043 2143 Dihedral : 5.831 23.964 1649 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.14 % Allowed : 17.48 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.49 (0.21), residues: 1522 helix: -0.12 (0.47), residues: 119 sheet: -0.85 (0.19), residues: 673 loop : -1.16 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 210 HIS 0.009 0.001 HIS B 445 PHE 0.029 0.003 PHE A 67 TYR 0.017 0.002 TYR B 304 ARG 0.008 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3941 (t0) cc_final: 0.3702 (t0) REVERT: A 839 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: A 859 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: A 900 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7567 (mpt180) outliers start: 42 outliers final: 16 residues processed: 117 average time/residue: 1.0599 time to fit residues: 138.7444 Evaluate side-chains 101 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1013 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN B 99 ASN B 445 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12251 Z= 0.211 Angle : 0.668 11.240 16610 Z= 0.343 Chirality : 0.048 0.188 1888 Planarity : 0.004 0.042 2143 Dihedral : 5.412 19.642 1649 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.09 % Allowed : 18.89 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.38 (0.21), residues: 1522 helix: 0.05 (0.50), residues: 120 sheet: -0.77 (0.20), residues: 632 loop : -1.12 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.005 0.001 HIS A 905 PHE 0.032 0.002 PHE A 67 TYR 0.015 0.002 TYR A 935 ARG 0.007 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3663 (t0) cc_final: 0.3426 (t0) REVERT: A 877 ASN cc_start: 0.8080 (p0) cc_final: 0.7611 (p0) REVERT: B 231 VAL cc_start: 0.6937 (t) cc_final: 0.6730 (m) outliers start: 28 outliers final: 13 residues processed: 113 average time/residue: 1.0425 time to fit residues: 132.2772 Evaluate side-chains 98 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12251 Z= 0.226 Angle : 0.678 11.654 16610 Z= 0.344 Chirality : 0.048 0.181 1888 Planarity : 0.004 0.042 2143 Dihedral : 5.303 19.620 1649 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.87 % Allowed : 19.27 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.34 (0.21), residues: 1522 helix: 0.02 (0.49), residues: 123 sheet: -0.73 (0.20), residues: 636 loop : -1.09 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.007 0.001 HIS B 445 PHE 0.027 0.002 PHE A 67 TYR 0.017 0.002 TYR B 295 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3856 (t0) cc_final: 0.3641 (t0) REVERT: A 877 ASN cc_start: 0.8052 (p0) cc_final: 0.7585 (p0) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 1.0515 time to fit residues: 122.5882 Evaluate side-chains 100 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12251 Z= 0.218 Angle : 0.690 12.950 16610 Z= 0.350 Chirality : 0.048 0.181 1888 Planarity : 0.004 0.043 2143 Dihedral : 5.276 19.170 1649 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.57 % Allowed : 19.72 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.29 (0.21), residues: 1522 helix: 0.12 (0.49), residues: 123 sheet: -0.68 (0.20), residues: 627 loop : -1.08 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.008 0.001 HIS A 600 PHE 0.034 0.002 PHE A1097 TYR 0.017 0.002 TYR A 935 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3779 (t0) cc_final: 0.3572 (t0) REVERT: A 877 ASN cc_start: 0.8076 (p0) cc_final: 0.7579 (p0) REVERT: A 900 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7594 (mpt-90) REVERT: B 425 CYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6586 (p) outliers start: 21 outliers final: 14 residues processed: 98 average time/residue: 1.0027 time to fit residues: 111.2680 Evaluate side-chains 94 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12251 Z= 0.365 Angle : 0.776 12.538 16610 Z= 0.396 Chirality : 0.050 0.169 1888 Planarity : 0.005 0.045 2143 Dihedral : 5.772 22.763 1649 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.57 % Allowed : 20.01 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: -0.10 (0.47), residues: 121 sheet: -0.90 (0.19), residues: 651 loop : -1.26 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 407 HIS 0.007 0.002 HIS A 600 PHE 0.031 0.003 PHE A 67 TYR 0.020 0.002 TYR B 304 ARG 0.005 0.001 ARG A 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 835 MET cc_start: 0.6749 (ttt) cc_final: 0.6500 (ttt) REVERT: A 877 ASN cc_start: 0.8306 (p0) cc_final: 0.7960 (p0) REVERT: B 425 CYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6655 (p) outliers start: 21 outliers final: 15 residues processed: 92 average time/residue: 1.0412 time to fit residues: 107.1292 Evaluate side-chains 89 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.116913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.101197 restraints weight = 44193.727| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 4.33 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12251 Z= 0.222 Angle : 0.700 12.343 16610 Z= 0.355 Chirality : 0.048 0.180 1888 Planarity : 0.004 0.044 2143 Dihedral : 5.394 21.907 1649 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.64 % Allowed : 19.87 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: -0.02 (0.49), residues: 123 sheet: -0.84 (0.20), residues: 629 loop : -1.19 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 561 HIS 0.006 0.001 HIS A 600 PHE 0.045 0.002 PHE A1097 TYR 0.018 0.002 TYR A 935 ARG 0.004 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.06 seconds wall clock time: 68 minutes 12.68 seconds (4092.68 seconds total)