Starting phenix.real_space_refine on Sat Aug 23 12:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajn_15485/08_2025/8ajn_15485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajn_15485/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ajn_15485/08_2025/8ajn_15485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajn_15485/08_2025/8ajn_15485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ajn_15485/08_2025/8ajn_15485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajn_15485/08_2025/8ajn_15485.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.24 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: 0.86 Conformation dependent library (CDL) restraints added in 540.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.55 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: 2.18 Time building geometry restraints manager: 1.19 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 68 TYR 0.045 0.006 TYR B 295 PHE 0.049 0.005 PHE A 851 TRP 0.054 0.006 TRP B 210 HIS 0.010 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00603 (12251) covalent geometry : angle 0.93984 (16610) SS BOND : bond 0.00524 ( 1) SS BOND : angle 0.32504 ( 2) hydrogen bonds : bond 0.18427 ( 462) hydrogen bonds : angle 8.81810 ( 1278) *********************** 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 : 0.321 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: 0.5240 (mtp) REVERT: A 900 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7597 (mmt90) REVERT: A 969 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5651 (pp20) REVERT: A 1036 MET cc_start: 0.5883 (tmt) cc_final: 0.5490 (tmt) REVERT: A 1105 MET cc_start: 0.5906 (mtt) cc_final: 0.5571 (mtt) REVERT: B 197 MET cc_start: 0.3753 (mtm) cc_final: 0.3492 (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: 0.5487 time to fit residues: 138.2097 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 : 0.490 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 778 HIS A 809 GLN A 952 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.122215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.106120 restraints weight = 42879.389| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 4.49 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12252 Z= 0.145 Angle : 0.700 8.687 16612 Z= 0.369 Chirality : 0.049 0.177 1888 Planarity : 0.005 0.090 2143 Dihedral : 6.392 85.941 1662 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 10.23 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1522 helix: -0.28 (0.47), residues: 117 sheet: -0.39 (0.19), residues: 670 loop : -0.72 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 337 TYR 0.017 0.002 TYR A 678 PHE 0.030 0.002 PHE A 851 TRP 0.015 0.001 TRP B 97 HIS 0.010 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00322 (12251) covalent geometry : angle 0.70046 (16610) SS BOND : bond 0.00427 ( 1) SS BOND : angle 0.79007 ( 2) hydrogen bonds : bond 0.04458 ( 462) hydrogen bonds : angle 6.58416 ( 1278) *********************** 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 163 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.5170 (t0) cc_final: 0.4967 (t0) REVERT: A 167 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.6818 (p) REVERT: A 218 MET cc_start: 0.6016 (mtp) cc_final: 0.5464 (mtp) REVERT: A 786 VAL cc_start: 0.6633 (t) cc_final: 0.6424 (m) REVERT: A 826 ASN cc_start: 0.6929 (m110) cc_final: 0.6704 (m110) REVERT: A 900 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7968 (mpt90) REVERT: B 195 ASP cc_start: 0.7113 (m-30) cc_final: 0.6829 (m-30) REVERT: B 197 MET cc_start: 0.4131 (mtm) cc_final: 0.3913 (tpp) outliers start: 35 outliers final: 8 residues processed: 151 average time/residue: 0.4289 time to fit residues: 71.6665 Evaluate side-chains 104 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL 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 Chi-restraints excluded: chain B residue 102 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.117746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.101748 restraints weight = 44461.061| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 4.45 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12252 Z= 0.202 Angle : 0.703 9.426 16612 Z= 0.367 Chirality : 0.049 0.181 1888 Planarity : 0.005 0.056 2143 Dihedral : 5.559 21.791 1649 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.99 % Allowed : 12.77 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.21), residues: 1522 helix: -0.07 (0.49), residues: 122 sheet: -0.35 (0.20), residues: 661 loop : -0.81 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 739 TYR 0.016 0.002 TYR A 828 PHE 0.032 0.002 PHE A 851 TRP 0.015 0.002 TRP B 210 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00465 (12251) covalent geometry : angle 0.70309 (16610) SS BOND : bond 0.00632 ( 1) SS BOND : angle 0.86047 ( 2) hydrogen bonds : bond 0.04477 ( 462) hydrogen bonds : angle 6.56806 ( 1278) *********************** 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 138 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7371 (tp) cc_final: 0.7122 (pt) REVERT: A 167 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7071 (m) REVERT: A 218 MET cc_start: 0.6235 (mtp) cc_final: 0.5742 (mtp) REVERT: A 231 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 718 TYR cc_start: 0.9048 (m-80) cc_final: 0.8707 (m-80) REVERT: A 839 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: A 900 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7802 (mmt90) REVERT: A 1111 ASN cc_start: 0.7800 (p0) cc_final: 0.7525 (m-40) outliers start: 40 outliers final: 9 residues processed: 126 average time/residue: 0.3648 time to fit residues: 51.5447 Evaluate side-chains 99 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE 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 839 GLU 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 57 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 72 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 952 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.119427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.103509 restraints weight = 43957.576| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 4.44 r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12252 Z= 0.140 Angle : 0.650 10.563 16612 Z= 0.335 Chirality : 0.047 0.194 1888 Planarity : 0.004 0.044 2143 Dihedral : 5.262 18.194 1649 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.91 % Allowed : 14.19 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.21), residues: 1522 helix: -0.03 (0.48), residues: 124 sheet: -0.42 (0.20), residues: 674 loop : -0.75 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.023 0.002 TYR A 678 PHE 0.024 0.002 PHE A 851 TRP 0.011 0.001 TRP B 210 HIS 0.006 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00321 (12251) covalent geometry : angle 0.64981 (16610) SS BOND : bond 0.00465 ( 1) SS BOND : angle 0.65885 ( 2) hydrogen bonds : bond 0.03762 ( 462) hydrogen bonds : angle 6.24958 ( 1278) *********************** 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 139 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7129 (m) REVERT: A 218 MET cc_start: 0.6169 (mtp) cc_final: 0.5710 (mtp) REVERT: A 231 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 718 TYR cc_start: 0.8997 (m-80) cc_final: 0.8630 (m-80) REVERT: A 839 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: A 877 ASN cc_start: 0.8573 (p0) cc_final: 0.8094 (p0) REVERT: A 900 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7778 (mmt90) REVERT: A 1111 ASN cc_start: 0.7738 (p0) cc_final: 0.7468 (m-40) outliers start: 39 outliers final: 13 residues processed: 130 average time/residue: 0.3995 time to fit residues: 58.2907 Evaluate side-chains 104 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE 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 618 ILE Chi-restraints excluded: chain A residue 839 GLU 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 1065 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 86 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** 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 = 0.4803 r_free = 0.4803 target = 0.118458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.102671 restraints weight = 44178.231| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 4.36 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12252 Z= 0.148 Angle : 0.641 9.313 16612 Z= 0.331 Chirality : 0.047 0.183 1888 Planarity : 0.004 0.047 2143 Dihedral : 5.166 18.376 1649 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.24 % Allowed : 15.76 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.21), residues: 1522 helix: 0.04 (0.49), residues: 124 sheet: -0.45 (0.20), residues: 663 loop : -0.82 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.019 0.002 TYR A 678 PHE 0.027 0.002 PHE A 67 TRP 0.010 0.001 TRP B 279 HIS 0.005 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00342 (12251) covalent geometry : angle 0.64079 (16610) SS BOND : bond 0.00501 ( 1) SS BOND : angle 0.76309 ( 2) hydrogen bonds : bond 0.03735 ( 462) hydrogen bonds : angle 6.17724 ( 1278) *********************** 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 123 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7007 (p) REVERT: A 171 TYR cc_start: 0.6799 (m-80) cc_final: 0.6387 (m-80) REVERT: A 218 MET cc_start: 0.6140 (mtp) cc_final: 0.5714 (mtp) REVERT: A 226 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6348 (t80) REVERT: A 231 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7661 (pp) REVERT: A 877 ASN cc_start: 0.8655 (p0) cc_final: 0.8226 (p0) REVERT: A 900 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7755 (mpt90) REVERT: A 1111 ASN cc_start: 0.7736 (p0) cc_final: 0.7509 (m-40) REVERT: A 1120 MET cc_start: 0.7147 (pmm) cc_final: 0.6920 (pmm) outliers start: 30 outliers final: 11 residues processed: 114 average time/residue: 0.4225 time to fit residues: 54.3849 Evaluate side-chains 94 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 231 ILE 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 618 ILE 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 1065 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 19 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 131 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 143 optimal weight: 0.0170 chunk 58 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.118675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.102506 restraints weight = 43581.889| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 4.45 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12252 Z= 0.138 Angle : 0.629 10.006 16612 Z= 0.324 Chirality : 0.047 0.183 1888 Planarity : 0.004 0.042 2143 Dihedral : 5.047 17.919 1649 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.54 % Allowed : 15.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.21), residues: 1522 helix: 0.21 (0.50), residues: 117 sheet: -0.51 (0.20), residues: 672 loop : -0.79 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1057 TYR 0.019 0.002 TYR A 678 PHE 0.028 0.002 PHE A 67 TRP 0.009 0.001 TRP B 210 HIS 0.005 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00308 (12251) covalent geometry : angle 0.62944 (16610) SS BOND : bond 0.00441 ( 1) SS BOND : angle 0.71912 ( 2) hydrogen bonds : bond 0.03571 ( 462) hydrogen bonds : angle 6.09780 ( 1278) *********************** 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 124 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7103 (p) REVERT: A 171 TYR cc_start: 0.6835 (m-80) cc_final: 0.6574 (m-80) REVERT: A 218 MET cc_start: 0.6090 (mtp) cc_final: 0.5678 (mtp) REVERT: A 231 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7588 (pp) REVERT: A 873 MET cc_start: 0.2296 (mtt) cc_final: 0.2091 (mtt) REVERT: A 900 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7775 (mmt90) outliers start: 34 outliers final: 14 residues processed: 113 average time/residue: 0.4062 time to fit residues: 51.1433 Evaluate side-chains 96 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 288 GLU 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 618 ILE Chi-restraints excluded: chain A residue 861 VAL 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 1065 VAL Chi-restraints excluded: chain A residue 1074 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 46 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.116009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.099746 restraints weight = 43705.366| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 4.44 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12252 Z= 0.209 Angle : 0.708 8.861 16612 Z= 0.362 Chirality : 0.048 0.171 1888 Planarity : 0.005 0.046 2143 Dihedral : 5.379 20.252 1649 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.39 % Allowed : 17.03 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.21), residues: 1522 helix: 0.02 (0.50), residues: 117 sheet: -0.70 (0.19), residues: 662 loop : -0.90 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1080 TYR 0.015 0.002 TYR B 304 PHE 0.031 0.002 PHE A 67 TRP 0.009 0.002 TRP B 210 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00472 (12251) covalent geometry : angle 0.70752 (16610) SS BOND : bond 0.00603 ( 1) SS BOND : angle 1.00344 ( 2) hydrogen bonds : bond 0.04021 ( 462) hydrogen bonds : angle 6.48525 ( 1278) *********************** 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 116 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7219 (p) REVERT: A 218 MET cc_start: 0.6185 (mtp) cc_final: 0.5816 (mtp) REVERT: A 231 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7661 (pp) REVERT: A 877 ASN cc_start: 0.8927 (p0) cc_final: 0.8600 (p0) REVERT: A 900 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7757 (mmt90) outliers start: 32 outliers final: 15 residues processed: 108 average time/residue: 0.3939 time to fit residues: 47.9275 Evaluate side-chains 95 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 367 LEU 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 618 ILE 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 1074 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.115865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.099601 restraints weight = 43798.107| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 4.43 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12252 Z= 0.210 Angle : 0.724 11.775 16612 Z= 0.369 Chirality : 0.049 0.177 1888 Planarity : 0.005 0.055 2143 Dihedral : 5.524 21.477 1649 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.46 % Allowed : 17.55 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.21), residues: 1522 helix: -0.09 (0.48), residues: 116 sheet: -0.71 (0.20), residues: 646 loop : -1.06 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1080 TYR 0.017 0.002 TYR A 171 PHE 0.037 0.002 PHE A1097 TRP 0.011 0.002 TRP A1047 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00474 (12251) covalent geometry : angle 0.72410 (16610) SS BOND : bond 0.00637 ( 1) SS BOND : angle 0.93207 ( 2) hydrogen bonds : bond 0.03965 ( 462) hydrogen bonds : angle 6.59580 ( 1278) *********************** 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: 33 poor density : 79 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7231 (p) REVERT: A 218 MET cc_start: 0.6170 (mtp) cc_final: 0.5829 (mtp) REVERT: A 231 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7676 (pp) REVERT: A 840 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: A 877 ASN cc_start: 0.8986 (p0) cc_final: 0.8710 (p0) REVERT: A 900 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7708 (mpt90) REVERT: A 910 MET cc_start: 0.6301 (mtt) cc_final: 0.6019 (mmt) REVERT: B 425 CYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6322 (p) outliers start: 33 outliers final: 15 residues processed: 103 average time/residue: 0.4376 time to fit residues: 50.3082 Evaluate side-chains 93 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 854 SER 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 1074 ARG 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 2 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.118347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.102218 restraints weight = 43582.455| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 4.44 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12252 Z= 0.141 Angle : 0.689 11.071 16612 Z= 0.348 Chirality : 0.048 0.186 1888 Planarity : 0.004 0.053 2143 Dihedral : 5.242 25.206 1649 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.79 % Allowed : 18.22 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.21), residues: 1522 helix: -0.02 (0.49), residues: 117 sheet: -0.66 (0.20), residues: 628 loop : -0.97 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1080 TYR 0.013 0.002 TYR A 913 PHE 0.027 0.002 PHE A 67 TRP 0.014 0.001 TRP B 210 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00323 (12251) covalent geometry : angle 0.68936 (16610) SS BOND : bond 0.00441 ( 1) SS BOND : angle 0.68413 ( 2) hydrogen bonds : bond 0.03496 ( 462) hydrogen bonds : angle 6.29872 ( 1278) *********************** 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: 24 poor density : 80 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7347 (p) REVERT: A 171 TYR cc_start: 0.6732 (m-80) cc_final: 0.6393 (m-80) REVERT: A 218 MET cc_start: 0.5849 (mtp) cc_final: 0.5550 (mtp) REVERT: A 231 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 350 MET cc_start: 0.5920 (ttt) cc_final: 0.5357 (ptm) REVERT: A 740 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6834 (pt) REVERT: A 840 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5845 (mp0) REVERT: A 859 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: A 877 ASN cc_start: 0.8894 (p0) cc_final: 0.8524 (p0) REVERT: A 900 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7681 (mmt90) REVERT: A 910 MET cc_start: 0.6086 (mtt) cc_final: 0.5870 (mmt) REVERT: A 1014 MET cc_start: 0.4828 (ptt) cc_final: 0.3413 (mmt) outliers start: 24 outliers final: 10 residues processed: 100 average time/residue: 0.4018 time to fit residues: 44.8192 Evaluate side-chains 92 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 296 THR 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 740 ILE Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 859 GLN 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 1012 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.116758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.100716 restraints weight = 44294.164| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 4.37 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12252 Z= 0.187 Angle : 0.729 11.781 16612 Z= 0.368 Chirality : 0.048 0.184 1888 Planarity : 0.005 0.058 2143 Dihedral : 5.411 24.752 1649 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.64 % Allowed : 18.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.21), residues: 1522 helix: 0.04 (0.49), residues: 116 sheet: -0.69 (0.20), residues: 638 loop : -1.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1080 TYR 0.015 0.002 TYR B 304 PHE 0.039 0.002 PHE A1097 TRP 0.011 0.002 TRP B 210 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00426 (12251) covalent geometry : angle 0.72916 (16610) SS BOND : bond 0.00532 ( 1) SS BOND : angle 0.85142 ( 2) hydrogen bonds : bond 0.03801 ( 462) hydrogen bonds : angle 6.47966 ( 1278) ********************** 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 98 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7381 (p) REVERT: A 171 TYR cc_start: 0.6762 (m-80) cc_final: 0.6477 (m-80) REVERT: A 231 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7605 (pp) REVERT: A 740 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6897 (pt) REVERT: A 840 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: A 859 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: A 877 ASN cc_start: 0.8920 (p0) cc_final: 0.8581 (p0) REVERT: A 900 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7720 (mpt90) REVERT: A 1014 MET cc_start: 0.5111 (ptt) cc_final: 0.3482 (mmt) outliers start: 22 outliers final: 11 residues processed: 95 average time/residue: 0.4018 time to fit residues: 42.7634 Evaluate side-chains 86 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 859 GLN 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 B residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 117 optimal weight: 0.0170 chunk 136 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.117546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.101875 restraints weight = 43636.184| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 4.31 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12252 Z= 0.151 Angle : 0.706 13.006 16612 Z= 0.356 Chirality : 0.048 0.200 1888 Planarity : 0.004 0.053 2143 Dihedral : 5.275 24.723 1649 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.94 % Allowed : 18.60 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.21), residues: 1522 helix: 0.08 (0.49), residues: 117 sheet: -0.66 (0.20), residues: 635 loop : -1.07 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1080 TYR 0.015 0.002 TYR A 678 PHE 0.024 0.002 PHE B 188 TRP 0.012 0.001 TRP B 210 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00348 (12251) covalent geometry : angle 0.70582 (16610) SS BOND : bond 0.00448 ( 1) SS BOND : angle 0.83282 ( 2) hydrogen bonds : bond 0.03537 ( 462) hydrogen bonds : angle 6.33945 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.06 seconds wall clock time: 50 minutes 42.86 seconds (3042.86 seconds total)