Starting phenix.real_space_refine on Wed Jul 30 08:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajn_15485/07_2025/8ajn_15485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajn_15485/07_2025/8ajn_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_15485/07_2025/8ajn_15485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajn_15485/07_2025/8ajn_15485.map" model { file = "/net/cci-nas-00/data/ceres_data/8ajn_15485/07_2025/8ajn_15485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajn_15485/07_2025/8ajn_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-5711/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: 7.94, per 1000 atoms: 0.66 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: 2.91 Conformation dependent library (CDL) restraints added in 1.8 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: 2.25 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: 6.60 Time building geometry restraints manager: 3.47 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: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.060 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.250 ------------------------------------------------------------------------------- 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 12252 Z= 0.317 Angle : 0.940 7.553 16612 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 Details of bonding type rmsd hydrogen bonds : bond 0.18427 ( 462) hydrogen bonds : angle 8.81810 ( 1278) SS BOND : bond 0.00524 ( 1) SS BOND : angle 0.32504 ( 2) covalent geometry : bond 0.00603 (12251) covalent geometry : angle 0.93984 (16610) *********************** 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 : 1.492 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: 1.4300 time to fit residues: 360.3101 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 : 1.316 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.118005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.101773 restraints weight = 42985.373| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 4.38 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 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 12252 Z= 0.201 Angle : 0.732 9.139 16612 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 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 462) hydrogen bonds : angle 6.88904 ( 1278) SS BOND : bond 0.00622 ( 1) SS BOND : angle 0.98589 ( 2) covalent geometry : bond 0.00455 (12251) covalent geometry : angle 0.73218 (16610) *********************** 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 : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.6931 (p) REVERT: A 218 MET cc_start: 0.6211 (mtp) cc_final: 0.5639 (mtp) REVERT: A 826 ASN cc_start: 0.7214 (m110) cc_final: 0.6995 (m110) REVERT: A 900 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7803 (mmt90) REVERT: A 1105 MET cc_start: 0.5763 (mtt) cc_final: 0.5536 (mtt) REVERT: B 197 MET cc_start: 0.4118 (mtm) cc_final: 0.3907 (tpp) outliers start: 38 outliers final: 8 residues processed: 149 average time/residue: 1.0301 time to fit residues: 170.6498 Evaluate side-chains 98 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL 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 47 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 0.0030 overall best weight: 1.3592 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.117612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.101432 restraints weight = 44257.746| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 4.43 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12252 Z= 0.178 Angle : 0.686 10.110 16612 Z= 0.357 Chirality : 0.048 0.183 1888 Planarity : 0.004 0.041 2143 Dihedral : 5.620 22.722 1649 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.84 % Allowed : 13.07 % Favored : 84.09 % 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: -0.97 (0.21), residues: 1522 helix: -0.14 (0.48), residues: 119 sheet: -0.39 (0.19), residues: 669 loop : -0.87 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 210 HIS 0.004 0.001 HIS A 905 PHE 0.030 0.002 PHE A 851 TYR 0.021 0.002 TYR A 828 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 462) hydrogen bonds : angle 6.67653 ( 1278) SS BOND : bond 0.00595 ( 1) SS BOND : angle 0.82644 ( 2) covalent geometry : bond 0.00407 (12251) covalent geometry : angle 0.68611 (16610) *********************** 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 137 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7134 (m) REVERT: A 218 MET cc_start: 0.6289 (mtp) cc_final: 0.5794 (mtp) REVERT: A 900 ARG cc_start: 0.8117 (ttp-170) cc_final: 0.7753 (mmt90) REVERT: A 1128 ASP cc_start: 0.6634 (m-30) cc_final: 0.6339 (m-30) outliers start: 38 outliers final: 11 residues processed: 127 average time/residue: 0.9572 time to fit residues: 137.0440 Evaluate side-chains 100 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 167 VAL 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 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 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: 1.9990 chunk 65 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 125 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.117439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.101282 restraints weight = 43022.341| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 4.39 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12252 Z= 0.175 Angle : 0.683 9.980 16612 Z= 0.352 Chirality : 0.048 0.183 1888 Planarity : 0.004 0.042 2143 Dihedral : 5.508 22.577 1649 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.20 % 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: -1.13 (0.21), residues: 1522 helix: -0.17 (0.47), residues: 127 sheet: -0.47 (0.19), residues: 659 loop : -1.02 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.005 0.001 HIS A 905 PHE 0.026 0.002 PHE A 851 TYR 0.024 0.002 TYR A 678 ARG 0.003 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 462) hydrogen bonds : angle 6.58184 ( 1278) SS BOND : bond 0.00601 ( 1) SS BOND : angle 0.89762 ( 2) covalent geometry : bond 0.00400 (12251) covalent geometry : angle 0.68273 (16610) *********************** 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 126 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7216 (m) REVERT: A 218 MET cc_start: 0.6262 (mtp) cc_final: 0.5759 (mtp) REVERT: A 839 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: A 877 ASN cc_start: 0.8712 (p0) cc_final: 0.8303 (p0) REVERT: A 900 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7757 (mpt90) REVERT: A 1128 ASP cc_start: 0.6515 (m-30) cc_final: 0.6226 (m-30) outliers start: 37 outliers final: 13 residues processed: 118 average time/residue: 1.0552 time to fit residues: 138.8371 Evaluate side-chains 102 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL 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 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 Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 61 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 810 ASN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.113527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.097361 restraints weight = 44484.433| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 4.50 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 12252 Z= 0.303 Angle : 0.808 10.167 16612 Z= 0.420 Chirality : 0.051 0.182 1888 Planarity : 0.005 0.045 2143 Dihedral : 6.154 26.207 1649 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.06 % Allowed : 15.68 % Favored : 81.25 % 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: -0.28 (0.47), residues: 117 sheet: -0.81 (0.19), residues: 655 loop : -1.15 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 210 HIS 0.008 0.002 HIS A 22 PHE 0.034 0.003 PHE A 851 TYR 0.025 0.003 TYR B 295 ARG 0.006 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 462) hydrogen bonds : angle 7.35742 ( 1278) SS BOND : bond 0.00841 ( 1) SS BOND : angle 1.32766 ( 2) covalent geometry : bond 0.00683 (12251) covalent geometry : angle 0.80754 (16610) *********************** 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 134 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7167 (p) REVERT: A 218 MET cc_start: 0.6297 (mtp) cc_final: 0.5844 (mtp) REVERT: A 839 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: A 1012 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 1111 ASN cc_start: 0.7787 (p0) cc_final: 0.7440 (m-40) REVERT: A 1128 ASP cc_start: 0.6667 (m-30) cc_final: 0.6358 (m-30) REVERT: B 102 GLN cc_start: 0.6553 (mt0) cc_final: 0.6336 (mt0) outliers start: 41 outliers final: 12 residues processed: 127 average time/residue: 1.0175 time to fit residues: 145.0008 Evaluate side-chains 102 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL 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 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 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 B residue 411 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 90 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 = 0.4757 r_free = 0.4757 target = 0.116124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.100167 restraints weight = 44320.944| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 4.36 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12252 Z= 0.161 Angle : 0.681 10.384 16612 Z= 0.349 Chirality : 0.048 0.207 1888 Planarity : 0.004 0.043 2143 Dihedral : 5.588 24.270 1649 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % 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: -1.42 (0.21), residues: 1522 helix: -0.07 (0.49), residues: 120 sheet: -0.85 (0.19), residues: 653 loop : -1.06 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 210 HIS 0.006 0.001 HIS A 905 PHE 0.032 0.002 PHE A 67 TYR 0.018 0.002 TYR A 678 ARG 0.003 0.000 ARG A1074 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 462) hydrogen bonds : angle 6.82591 ( 1278) SS BOND : bond 0.00540 ( 1) SS BOND : angle 0.79972 ( 2) covalent geometry : bond 0.00362 (12251) covalent geometry : angle 0.68116 (16610) *********************** 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 128 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7118 (p) REVERT: A 171 TYR cc_start: 0.6911 (m-80) cc_final: 0.6511 (m-80) REVERT: A 218 MET cc_start: 0.6109 (mtp) cc_final: 0.5669 (mtp) REVERT: A 839 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: A 873 MET cc_start: 0.2527 (mtt) cc_final: 0.2309 (mtt) REVERT: A 877 ASN cc_start: 0.8929 (p0) cc_final: 0.8645 (p0) REVERT: A 1012 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 1111 ASN cc_start: 0.7683 (p0) cc_final: 0.7392 (m-40) REVERT: A 1128 ASP cc_start: 0.6557 (m-30) cc_final: 0.6244 (m-30) outliers start: 34 outliers final: 14 residues processed: 120 average time/residue: 0.9923 time to fit residues: 133.3479 Evaluate side-chains 103 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 296 THR 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 410 LEU Chi-restraints excluded: chain A residue 614 PHE 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 1036 MET Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 130 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** B 90 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 = 0.4740 r_free = 0.4740 target = 0.115915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.099796 restraints weight = 44325.269| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 4.40 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12252 Z= 0.196 Angle : 0.702 9.786 16612 Z= 0.362 Chirality : 0.048 0.178 1888 Planarity : 0.004 0.044 2143 Dihedral : 5.613 25.992 1649 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.76 % Allowed : 18.45 % Favored : 78.79 % 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: 0.04 (0.49), residues: 119 sheet: -0.95 (0.19), residues: 664 loop : -1.06 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 210 HIS 0.006 0.001 HIS A 905 PHE 0.030 0.002 PHE A 67 TYR 0.019 0.002 TYR B 295 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 462) hydrogen bonds : angle 6.88784 ( 1278) SS BOND : bond 0.00623 ( 1) SS BOND : angle 1.02283 ( 2) covalent geometry : bond 0.00443 (12251) covalent geometry : angle 0.70205 (16610) *********************** 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 129 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7210 (tp) cc_final: 0.6975 (pt) REVERT: A 167 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7284 (p) REVERT: A 171 TYR cc_start: 0.6965 (m-80) cc_final: 0.6596 (m-80) REVERT: A 218 MET cc_start: 0.6035 (mtp) cc_final: 0.5653 (mtp) REVERT: A 839 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: A 877 ASN cc_start: 0.8978 (p0) cc_final: 0.8727 (p0) REVERT: A 910 MET cc_start: 0.6074 (mmm) cc_final: 0.5821 (mmt) REVERT: A 1012 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 1111 ASN cc_start: 0.7733 (p0) cc_final: 0.7401 (m-40) REVERT: A 1128 ASP cc_start: 0.6536 (m-30) cc_final: 0.6235 (m-30) REVERT: B 102 GLN cc_start: 0.6627 (mt0) cc_final: 0.6335 (mt0) REVERT: B 425 CYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6333 (p) outliers start: 37 outliers final: 16 residues processed: 119 average time/residue: 0.9713 time to fit residues: 129.2372 Evaluate side-chains 104 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP 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 839 GLU Chi-restraints excluded: chain A residue 854 SER 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 1109 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.098365 restraints weight = 45315.685| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 4.35 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12252 Z= 0.240 Angle : 0.763 10.817 16612 Z= 0.390 Chirality : 0.049 0.173 1888 Planarity : 0.005 0.045 2143 Dihedral : 5.800 26.829 1649 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.39 % Allowed : 18.89 % 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: -1.66 (0.21), residues: 1522 helix: -0.03 (0.48), residues: 118 sheet: -1.05 (0.19), residues: 660 loop : -1.22 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 407 HIS 0.007 0.001 HIS B 445 PHE 0.030 0.002 PHE A1097 TYR 0.020 0.002 TYR B 295 ARG 0.004 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 462) hydrogen bonds : angle 7.12460 ( 1278) SS BOND : bond 0.00716 ( 1) SS BOND : angle 1.21016 ( 2) covalent geometry : bond 0.00543 (12251) covalent geometry : angle 0.76276 (16610) *********************** 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 112 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7232 (p) REVERT: A 218 MET cc_start: 0.6108 (mtp) cc_final: 0.5874 (mtp) REVERT: A 859 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: A 1111 ASN cc_start: 0.7813 (p0) cc_final: 0.7432 (m-40) REVERT: A 1128 ASP cc_start: 0.6623 (m-30) cc_final: 0.6330 (m-30) REVERT: B 102 GLN cc_start: 0.6700 (mt0) cc_final: 0.6297 (mp10) REVERT: B 425 CYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6393 (p) outliers start: 32 outliers final: 18 residues processed: 104 average time/residue: 1.0959 time to fit residues: 126.4669 Evaluate side-chains 99 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE 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 Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.116650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.100894 restraints weight = 44360.958| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 4.31 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12252 Z= 0.151 Angle : 0.712 11.422 16612 Z= 0.360 Chirality : 0.048 0.196 1888 Planarity : 0.004 0.044 2143 Dihedral : 5.429 25.692 1649 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.72 % Allowed : 19.87 % 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: -1.55 (0.21), residues: 1522 helix: -0.07 (0.49), residues: 126 sheet: -0.98 (0.19), residues: 645 loop : -1.14 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 210 HIS 0.007 0.001 HIS A 600 PHE 0.025 0.002 PHE A 67 TYR 0.015 0.002 TYR A 913 ARG 0.006 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 462) hydrogen bonds : angle 6.72857 ( 1278) SS BOND : bond 0.00490 ( 1) SS BOND : angle 0.86000 ( 2) covalent geometry : bond 0.00345 (12251) covalent geometry : angle 0.71163 (16610) *********************** 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 112 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7307 (p) REVERT: A 859 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: A 877 ASN cc_start: 0.8953 (p0) cc_final: 0.8668 (p0) REVERT: A 987 GLU cc_start: 0.7658 (mp0) cc_final: 0.6557 (mm-30) REVERT: A 1014 MET cc_start: 0.4888 (ptt) cc_final: 0.3289 (mmt) REVERT: A 1128 ASP cc_start: 0.6468 (m-30) cc_final: 0.6182 (m-30) REVERT: B 425 CYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6308 (p) outliers start: 23 outliers final: 15 residues processed: 103 average time/residue: 1.1821 time to fit residues: 137.2288 Evaluate side-chains 96 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 296 THR 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 391 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE 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 1036 MET Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 98 LEU 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 61 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** B 99 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.117483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.101911 restraints weight = 44007.292| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 4.31 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12252 Z= 0.142 Angle : 0.700 11.589 16612 Z= 0.353 Chirality : 0.048 0.190 1888 Planarity : 0.004 0.044 2143 Dihedral : 5.253 19.491 1649 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.57 % Allowed : 20.76 % Favored : 77.67 % 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: -1.35 (0.21), residues: 1522 helix: 0.21 (0.50), residues: 123 sheet: -0.86 (0.19), residues: 657 loop : -1.01 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 407 HIS 0.007 0.001 HIS A 600 PHE 0.034 0.002 PHE A1097 TYR 0.017 0.002 TYR B 295 ARG 0.003 0.000 ARG A1074 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 462) hydrogen bonds : angle 6.57664 ( 1278) SS BOND : bond 0.00474 ( 1) SS BOND : angle 1.03314 ( 2) covalent geometry : bond 0.00327 (12251) covalent geometry : angle 0.70003 (16610) ********************** 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 99 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7354 (p) REVERT: A 859 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8525 (mp10) REVERT: A 873 MET cc_start: 0.2418 (mtt) cc_final: 0.2123 (mtt) REVERT: A 877 ASN cc_start: 0.8924 (p0) cc_final: 0.8582 (p0) REVERT: A 987 GLU cc_start: 0.7616 (mp0) cc_final: 0.6471 (mm-30) REVERT: A 1014 MET cc_start: 0.4990 (ptt) cc_final: 0.3377 (mmt) REVERT: A 1128 ASP cc_start: 0.6414 (m-30) cc_final: 0.6160 (m-30) REVERT: B 425 CYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6220 (p) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 1.0337 time to fit residues: 108.2907 Evaluate side-chains 87 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 296 THR 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 391 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 614 PHE 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 1036 MET 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 75 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.114783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.099071 restraints weight = 45105.545| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 4.30 r_work: 0.4273 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12252 Z= 0.243 Angle : 0.776 13.424 16612 Z= 0.394 Chirality : 0.049 0.180 1888 Planarity : 0.005 0.045 2143 Dihedral : 5.622 21.657 1649 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.49 % Allowed : 21.21 % Favored : 77.30 % 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: -1.58 (0.21), residues: 1522 helix: -0.04 (0.49), residues: 124 sheet: -0.96 (0.19), residues: 663 loop : -1.20 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 407 HIS 0.008 0.002 HIS B 445 PHE 0.033 0.002 PHE A 67 TYR 0.018 0.002 TYR B 304 ARG 0.005 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 462) hydrogen bonds : angle 6.98987 ( 1278) SS BOND : bond 0.00649 ( 1) SS BOND : angle 1.15877 ( 2) covalent geometry : bond 0.00552 (12251) covalent geometry : angle 0.77583 (16610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8365.31 seconds wall clock time: 147 minutes 55.98 seconds (8875.98 seconds total)