Starting phenix.real_space_refine on Mon Dec 30 12:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.map" model { file = "/net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfl_25092/12_2024/7sfl_25092.cif" } resolution = 3.87 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 82 5.16 5 Cl 2 4.86 5 C 8491 2.51 5 N 2137 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13014 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6479 Classifications: {'peptide': 829} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 799} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6493 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 800} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.41, per 1000 atoms: 0.65 Number of scatterers: 13014 At special positions: 0 Unit cell: (81.32, 156.22, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 82 16.00 O 2302 8.00 N 2137 7.00 C 8491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " 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: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 64.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.866A pdb=" N LEU A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 305 " --> pdb=" O VAL A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 305' Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.521A pdb=" N ALA A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 399 removed outlier: 4.459A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.626A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 455 removed outlier: 4.810A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 removed outlier: 3.641A pdb=" N THR A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 544 removed outlier: 4.574A pdb=" N LYS A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.736A pdb=" N MET A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 632 removed outlier: 4.002A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 605 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 642 removed outlier: 4.966A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 667 Processing helix chain 'A' and resid 670 through 699 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.508A pdb=" N ILE A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 762 through 779 removed outlier: 4.200A pdb=" N THR A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.627A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 removed outlier: 3.600A pdb=" N GLU A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.502A pdb=" N ILE A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix removed outlier: 3.568A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1079 removed outlier: 3.627A pdb=" N LEU A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 removed outlier: 3.652A pdb=" N ILE A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 3.551A pdb=" N LEU A1139 " --> pdb=" O THR A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.885A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.066A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.696A pdb=" N GLY B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 Processing helix chain 'B' and resid 430 through 455 removed outlier: 4.351A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.516A pdb=" N PHE B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 500 through 501 No H-bonds generated for 'chain 'B' and resid 500 through 501' Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 513 through 542 removed outlier: 3.566A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix removed outlier: 3.884A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.723A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 633 Proline residue: B 623 - end of helix removed outlier: 3.707A pdb=" N ASN B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 5.172A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 666 Processing helix chain 'B' and resid 670 through 699 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 730 Processing helix chain 'B' and resid 731 through 751 removed outlier: 4.193A pdb=" N TYR B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 758 removed outlier: 4.167A pdb=" N VAL B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP B 758 " --> pdb=" O PRO B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 780 removed outlier: 4.258A pdb=" N ASN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 780 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.845A pdb=" N LEU B 805 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 849 removed outlier: 3.583A pdb=" N GLU B 834 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.621A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1080 removed outlier: 4.234A pdb=" N ASP B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1108 Processing helix chain 'B' and resid 1119 through 1128 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 removed outlier: 4.019A pdb=" N ASN B1153 " --> pdb=" O GLN B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1191 Processing sheet with id=AA1, first strand: chain 'A' and resid 853 through 859 removed outlier: 7.594A pdb=" N MET A 818 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ALA A 856 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 820 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 858 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS A 822 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A 884 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 920 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 886 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 791 through 793 removed outlier: 3.522A pdb=" N ILE B 920 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE B1024 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE B1057 " --> pdb=" O ILE B1024 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B1026 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY B1059 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B1054 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819 removed outlier: 6.471A pdb=" N MET B 818 " --> pdb=" O PHE B 854 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 removed outlier: 6.025A pdb=" N HIS B 822 " --> pdb=" O VAL B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1113 736 hydrogen bonds defined for protein. 2175 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: 4.01 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4056 1.34 - 1.47: 3203 1.47 - 1.59: 5906 1.59 - 1.71: 2 1.71 - 1.84: 140 Bond restraints: 13307 Sorted by residual: bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C7 FUN A1301 " pdb=" C8 FUN A1301 " ideal model delta sigma weight residual 1.429 1.360 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N1 FUN A1301 " pdb=" S1 FUN A1301 " ideal model delta sigma weight residual 1.647 1.708 -0.061 2.00e-02 2.50e+03 9.17e+00 ... (remaining 13302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 17949 3.59 - 7.18: 92 7.18 - 10.76: 8 10.76 - 14.35: 0 14.35 - 17.94: 2 Bond angle restraints: 18051 Sorted by residual: angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.23 17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.25 17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA MET A 851 " pdb=" CB MET A 851 " pdb=" CG MET A 851 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N ILE A1081 " pdb=" CA ILE A1081 " pdb=" C ILE A1081 " ideal model delta sigma weight residual 112.29 109.37 2.92 9.40e-01 1.13e+00 9.62e+00 ... (remaining 18046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7113 17.84 - 35.67: 630 35.67 - 53.51: 92 53.51 - 71.35: 15 71.35 - 89.19: 7 Dihedral angle restraints: 7857 sinusoidal: 3072 harmonic: 4785 Sorted by residual: dihedral pdb=" CB CYS B 563 " pdb=" SG CYS B 563 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual -86.00 -154.94 68.94 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA ASN B 571 " pdb=" C ASN B 571 " pdb=" N PHE B 572 " pdb=" CA PHE B 572 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA A 505 " pdb=" C ALA A 505 " pdb=" N ASN A 506 " pdb=" CA ASN A 506 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 7854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1666 0.054 - 0.108: 366 0.108 - 0.162: 45 0.162 - 0.216: 3 0.216 - 0.270: 1 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CA GLN A 914 " pdb=" N GLN A 914 " pdb=" C GLN A 914 " pdb=" CB GLN A 914 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE A 747 " pdb=" CA ILE A 747 " pdb=" CG1 ILE A 747 " pdb=" CG2 ILE A 747 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ASP A 755 " pdb=" N ASP A 755 " pdb=" C ASP A 755 " pdb=" CB ASP A 755 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2078 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 461 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 462 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 495 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 496 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 655 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C TYR B 655 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR B 655 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 656 " -0.012 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 283 2.70 - 3.25: 14427 3.25 - 3.80: 21393 3.80 - 4.35: 26395 4.35 - 4.90: 43401 Nonbonded interactions: 105899 Sorted by model distance: nonbonded pdb=" OG SER A 701 " pdb=" OD1 ASN A 769 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN A 298 " pdb=" O GLY A 500 " model vdw 2.172 3.120 nonbonded pdb=" NH1 ARG A1151 " pdb=" OE2 GLU A1154 " model vdw 2.180 3.120 nonbonded pdb=" OD2 ASP B1032 " pdb=" OG1 THR B1036 " model vdw 2.191 3.040 nonbonded pdb=" OD2 ASP B1025 " pdb=" OG SER B1160 " model vdw 2.216 3.040 ... (remaining 105894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 287 through 1208 or resid 1301)) selection = (chain 'B' and (resid 287 through 1208 or resid 1301)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.720 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.004 0.111 13307 Z= 0.283 Angle : 0.732 17.940 18051 Z= 0.367 Chirality : 0.044 0.270 2081 Planarity : 0.005 0.066 2240 Dihedral : 13.509 89.187 4772 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1651 helix: 1.11 (0.16), residues: 950 sheet: -1.10 (0.48), residues: 122 loop : -2.17 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.023 0.002 PHE A 907 TYR 0.024 0.002 TYR B 751 ARG 0.005 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 321 VAL cc_start: 0.9374 (t) cc_final: 0.9078 (p) REVERT: A 326 MET cc_start: 0.7532 (tpp) cc_final: 0.7026 (tpp) REVERT: A 847 ILE cc_start: 0.8664 (pt) cc_final: 0.8420 (mm) REVERT: B 577 CYS cc_start: 0.5990 (m) cc_final: 0.5394 (m) REVERT: B 694 PHE cc_start: 0.8948 (t80) cc_final: 0.8682 (t80) REVERT: B 713 MET cc_start: 0.8171 (ppp) cc_final: 0.7683 (ppp) REVERT: B 825 MET cc_start: 0.8883 (mpp) cc_final: 0.8229 (mpp) REVERT: B 1101 ILE cc_start: 0.8138 (mt) cc_final: 0.7540 (mm) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.2091 time to fit residues: 105.1890 Evaluate side-chains 263 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 0.0020 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS B 589 ASN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13307 Z= 0.214 Angle : 0.654 9.420 18051 Z= 0.332 Chirality : 0.043 0.171 2081 Planarity : 0.004 0.063 2240 Dihedral : 6.138 85.856 1777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.08 % Allowed : 11.03 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1651 helix: 1.17 (0.16), residues: 991 sheet: -1.06 (0.47), residues: 124 loop : -2.23 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.031 0.002 PHE B 659 TYR 0.023 0.001 TYR A 739 ARG 0.006 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.7770 (mtt) cc_final: 0.7126 (ttm) REVERT: A 325 MET cc_start: 0.8181 (mtt) cc_final: 0.7948 (mtt) REVERT: A 326 MET cc_start: 0.7461 (tpp) cc_final: 0.7165 (tpp) REVERT: A 620 VAL cc_start: 0.8628 (t) cc_final: 0.8410 (m) REVERT: A 878 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7225 (mmt180) REVERT: A 1041 TYR cc_start: 0.8442 (t80) cc_final: 0.8058 (t80) REVERT: B 547 ASP cc_start: 0.8473 (m-30) cc_final: 0.8249 (m-30) REVERT: B 694 PHE cc_start: 0.8961 (t80) cc_final: 0.8498 (t80) REVERT: B 713 MET cc_start: 0.7644 (ppp) cc_final: 0.7098 (ppp) REVERT: B 1101 ILE cc_start: 0.8161 (mt) cc_final: 0.7708 (mm) outliers start: 29 outliers final: 16 residues processed: 302 average time/residue: 0.1995 time to fit residues: 95.2564 Evaluate side-chains 282 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1158 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 51 optimal weight: 0.0040 chunk 120 optimal weight: 5.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13307 Z= 0.216 Angle : 0.644 13.789 18051 Z= 0.324 Chirality : 0.043 0.167 2081 Planarity : 0.004 0.063 2240 Dihedral : 6.091 86.572 1777 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.58 % Allowed : 15.40 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1651 helix: 1.36 (0.17), residues: 960 sheet: -1.02 (0.47), residues: 124 loop : -2.14 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.046 0.002 PHE B 659 TYR 0.024 0.001 TYR A 739 ARG 0.005 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7499 (tpp) cc_final: 0.6984 (tpp) REVERT: A 569 LYS cc_start: 0.6644 (tppt) cc_final: 0.6385 (tppt) REVERT: A 878 ARG cc_start: 0.7528 (mmt180) cc_final: 0.7232 (mmt180) REVERT: B 694 PHE cc_start: 0.8863 (t80) cc_final: 0.8459 (t80) REVERT: B 713 MET cc_start: 0.7638 (ppp) cc_final: 0.7059 (ppp) outliers start: 36 outliers final: 25 residues processed: 301 average time/residue: 0.2345 time to fit residues: 111.9039 Evaluate side-chains 285 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 0.0000 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13307 Z= 0.202 Angle : 0.637 10.669 18051 Z= 0.319 Chirality : 0.043 0.200 2081 Planarity : 0.004 0.062 2240 Dihedral : 6.003 87.522 1777 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 3.44 % Allowed : 16.33 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1651 helix: 1.34 (0.16), residues: 964 sheet: -0.98 (0.48), residues: 120 loop : -2.19 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 704 HIS 0.005 0.001 HIS B 809 PHE 0.047 0.002 PHE B 659 TYR 0.016 0.001 TYR A 903 ARG 0.004 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8200 (mtt) cc_final: 0.7971 (mtt) REVERT: A 326 MET cc_start: 0.7408 (tpp) cc_final: 0.6928 (tpp) REVERT: A 569 LYS cc_start: 0.6593 (tppt) cc_final: 0.6329 (tppt) REVERT: A 748 TYR cc_start: 0.8075 (t80) cc_final: 0.7756 (t80) REVERT: B 547 ASP cc_start: 0.8512 (m-30) cc_final: 0.8199 (t0) REVERT: B 577 CYS cc_start: 0.5473 (m) cc_final: 0.4225 (m) REVERT: B 694 PHE cc_start: 0.8792 (t80) cc_final: 0.8501 (t80) REVERT: B 713 MET cc_start: 0.7653 (ppp) cc_final: 0.7164 (ppp) REVERT: B 772 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 825 MET cc_start: 0.8818 (mpp) cc_final: 0.8504 (mpp) REVERT: B 1040 PRO cc_start: 0.8757 (Cg_exo) cc_final: 0.8550 (Cg_endo) REVERT: B 1065 ILE cc_start: 0.8248 (mm) cc_final: 0.8030 (mm) REVERT: B 1101 ILE cc_start: 0.8246 (mt) cc_final: 0.7985 (mm) outliers start: 48 outliers final: 28 residues processed: 304 average time/residue: 0.2058 time to fit residues: 98.4677 Evaluate side-chains 276 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.0770 chunk 143 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13307 Z= 0.200 Angle : 0.636 9.935 18051 Z= 0.320 Chirality : 0.044 0.267 2081 Planarity : 0.004 0.062 2240 Dihedral : 5.937 88.474 1777 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 3.51 % Allowed : 18.05 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1651 helix: 1.37 (0.17), residues: 963 sheet: -1.01 (0.47), residues: 120 loop : -2.16 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.062 0.002 PHE B 659 TYR 0.018 0.001 TYR A 354 ARG 0.003 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 LYS cc_start: 0.6473 (tppt) cc_final: 0.6244 (tppt) REVERT: A 748 TYR cc_start: 0.8104 (t80) cc_final: 0.7762 (t80) REVERT: B 523 LEU cc_start: 0.8929 (mt) cc_final: 0.8650 (mt) REVERT: B 547 ASP cc_start: 0.8528 (m-30) cc_final: 0.8214 (t0) REVERT: B 577 CYS cc_start: 0.5347 (m) cc_final: 0.4136 (m) REVERT: B 694 PHE cc_start: 0.8780 (t80) cc_final: 0.8491 (t80) REVERT: B 713 MET cc_start: 0.7624 (ppp) cc_final: 0.7139 (ppp) REVERT: B 772 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: B 818 MET cc_start: 0.7879 (ttm) cc_final: 0.7516 (ttm) REVERT: B 825 MET cc_start: 0.8800 (mpp) cc_final: 0.8514 (mpp) REVERT: B 1043 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9199 (mm) REVERT: B 1065 ILE cc_start: 0.8237 (mm) cc_final: 0.8011 (mm) outliers start: 49 outliers final: 32 residues processed: 300 average time/residue: 0.2107 time to fit residues: 98.7026 Evaluate side-chains 287 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13307 Z= 0.202 Angle : 0.639 10.698 18051 Z= 0.322 Chirality : 0.045 0.385 2081 Planarity : 0.004 0.061 2240 Dihedral : 5.891 89.421 1777 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.72 % Allowed : 18.91 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1651 helix: 1.37 (0.17), residues: 962 sheet: -1.01 (0.48), residues: 120 loop : -2.21 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 892 HIS 0.004 0.001 HIS B 908 PHE 0.066 0.002 PHE B 659 TYR 0.016 0.001 TYR B 353 ARG 0.006 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6225 (tm-30) REVERT: A 569 LYS cc_start: 0.6530 (tppt) cc_final: 0.6292 (tppt) REVERT: A 748 TYR cc_start: 0.8106 (t80) cc_final: 0.7771 (t80) REVERT: B 523 LEU cc_start: 0.8921 (mt) cc_final: 0.8645 (mt) REVERT: B 547 ASP cc_start: 0.8525 (m-30) cc_final: 0.8229 (t0) REVERT: B 577 CYS cc_start: 0.5316 (m) cc_final: 0.4117 (m) REVERT: B 694 PHE cc_start: 0.8767 (t80) cc_final: 0.8494 (t80) REVERT: B 713 MET cc_start: 0.7644 (ppp) cc_final: 0.7135 (ppp) REVERT: B 772 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: B 776 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8105 (mtp85) REVERT: B 818 MET cc_start: 0.7920 (ttm) cc_final: 0.7581 (ttm) REVERT: B 825 MET cc_start: 0.8782 (mpp) cc_final: 0.8530 (mpp) REVERT: B 1043 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 1065 ILE cc_start: 0.8253 (mm) cc_final: 0.8036 (mm) REVERT: B 1184 MET cc_start: 0.7068 (tmm) cc_final: 0.6848 (tmm) outliers start: 52 outliers final: 31 residues processed: 303 average time/residue: 0.2123 time to fit residues: 99.2352 Evaluate side-chains 291 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13307 Z= 0.250 Angle : 0.677 10.572 18051 Z= 0.341 Chirality : 0.046 0.233 2081 Planarity : 0.004 0.060 2240 Dihedral : 5.895 88.889 1777 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.37 % Allowed : 20.20 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1651 helix: 1.34 (0.17), residues: 953 sheet: -1.28 (0.47), residues: 122 loop : -2.24 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.063 0.002 PHE B 659 TYR 0.023 0.001 TYR B 751 ARG 0.007 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 LYS cc_start: 0.6559 (tppt) cc_final: 0.6267 (tppt) REVERT: A 713 MET cc_start: 0.7560 (pmm) cc_final: 0.7285 (ppp) REVERT: A 748 TYR cc_start: 0.8154 (t80) cc_final: 0.7817 (t80) REVERT: B 523 LEU cc_start: 0.8904 (mt) cc_final: 0.8651 (mt) REVERT: B 547 ASP cc_start: 0.8557 (m-30) cc_final: 0.8267 (t0) REVERT: B 577 CYS cc_start: 0.5410 (m) cc_final: 0.4236 (m) REVERT: B 671 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8731 (tt) REVERT: B 694 PHE cc_start: 0.8811 (t80) cc_final: 0.8575 (t80) REVERT: B 713 MET cc_start: 0.7670 (ppp) cc_final: 0.7156 (ppp) REVERT: B 772 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: B 776 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8054 (mtp85) REVERT: B 1043 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9186 (mm) outliers start: 47 outliers final: 33 residues processed: 290 average time/residue: 0.2136 time to fit residues: 94.4649 Evaluate side-chains 279 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 843 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13307 Z= 0.221 Angle : 0.683 11.213 18051 Z= 0.341 Chirality : 0.045 0.186 2081 Planarity : 0.004 0.060 2240 Dihedral : 5.856 87.518 1777 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.44 % Allowed : 20.85 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1651 helix: 1.32 (0.17), residues: 958 sheet: -1.30 (0.46), residues: 124 loop : -2.22 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 892 HIS 0.004 0.001 HIS B 908 PHE 0.069 0.002 PHE B 659 TYR 0.024 0.001 TYR B 751 ARG 0.004 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.7520 (pmm) cc_final: 0.7276 (ppp) REVERT: A 748 TYR cc_start: 0.8120 (t80) cc_final: 0.7786 (t80) REVERT: A 757 ASN cc_start: 0.5447 (OUTLIER) cc_final: 0.5197 (p0) REVERT: B 523 LEU cc_start: 0.8955 (mt) cc_final: 0.8685 (mt) REVERT: B 547 ASP cc_start: 0.8465 (m-30) cc_final: 0.8166 (t0) REVERT: B 577 CYS cc_start: 0.5321 (m) cc_final: 0.4147 (m) REVERT: B 694 PHE cc_start: 0.8790 (t80) cc_final: 0.8586 (t80) REVERT: B 713 MET cc_start: 0.7661 (ppp) cc_final: 0.7135 (ppp) REVERT: B 772 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: B 776 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8121 (mtp85) REVERT: B 825 MET cc_start: 0.8700 (mpp) cc_final: 0.8204 (mmt) REVERT: B 835 MET cc_start: 0.8776 (mmt) cc_final: 0.8465 (mmm) REVERT: B 1043 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9184 (mm) REVERT: B 1065 ILE cc_start: 0.8262 (mm) cc_final: 0.8032 (mm) outliers start: 48 outliers final: 37 residues processed: 291 average time/residue: 0.2101 time to fit residues: 94.7384 Evaluate side-chains 283 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.0040 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 773 HIS ** B1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13307 Z= 0.215 Angle : 0.707 11.266 18051 Z= 0.351 Chirality : 0.046 0.366 2081 Planarity : 0.004 0.057 2240 Dihedral : 5.824 86.024 1777 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.37 % Allowed : 21.85 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1651 helix: 1.34 (0.17), residues: 957 sheet: -1.31 (0.46), residues: 124 loop : -2.24 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.067 0.002 PHE B 659 TYR 0.048 0.002 TYR A 354 ARG 0.004 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.7488 (pmm) cc_final: 0.7240 (ppp) REVERT: A 748 TYR cc_start: 0.8081 (t80) cc_final: 0.7772 (t80) REVERT: A 902 MET cc_start: 0.8707 (tpp) cc_final: 0.8217 (tpp) REVERT: B 523 LEU cc_start: 0.8921 (mt) cc_final: 0.8671 (mt) REVERT: B 547 ASP cc_start: 0.8436 (m-30) cc_final: 0.8148 (t0) REVERT: B 577 CYS cc_start: 0.5305 (m) cc_final: 0.3977 (m) REVERT: B 713 MET cc_start: 0.7523 (ppp) cc_final: 0.7064 (ppp) REVERT: B 772 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: B 776 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8075 (mtp85) REVERT: B 825 MET cc_start: 0.8755 (mpp) cc_final: 0.8210 (mmt) REVERT: B 835 MET cc_start: 0.8770 (mmt) cc_final: 0.8442 (mmm) REVERT: B 1043 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9195 (mm) REVERT: B 1053 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7872 (ttpp) REVERT: B 1065 ILE cc_start: 0.8281 (mm) cc_final: 0.8052 (mm) outliers start: 47 outliers final: 35 residues processed: 290 average time/residue: 0.2134 time to fit residues: 95.1065 Evaluate side-chains 287 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13307 Z= 0.227 Angle : 0.733 11.582 18051 Z= 0.364 Chirality : 0.046 0.381 2081 Planarity : 0.005 0.080 2240 Dihedral : 5.795 84.668 1777 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.87 % Allowed : 22.56 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1651 helix: 1.31 (0.17), residues: 964 sheet: -1.36 (0.46), residues: 124 loop : -2.24 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1028 HIS 0.004 0.001 HIS A 773 PHE 0.066 0.002 PHE B 659 TYR 0.025 0.001 TYR B 751 ARG 0.023 0.001 ARG A 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.7494 (pmm) cc_final: 0.7243 (ppp) REVERT: A 748 TYR cc_start: 0.8185 (t80) cc_final: 0.7836 (t80) REVERT: A 902 MET cc_start: 0.8700 (tpp) cc_final: 0.8454 (tpp) REVERT: B 523 LEU cc_start: 0.8895 (mt) cc_final: 0.8468 (mt) REVERT: B 547 ASP cc_start: 0.8439 (m-30) cc_final: 0.8168 (t0) REVERT: B 577 CYS cc_start: 0.5244 (m) cc_final: 0.3882 (m) REVERT: B 713 MET cc_start: 0.7617 (ppp) cc_final: 0.7020 (ppp) REVERT: B 772 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: B 776 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8105 (mtp85) REVERT: B 825 MET cc_start: 0.8761 (mpp) cc_final: 0.8173 (mmt) REVERT: B 835 MET cc_start: 0.8740 (mmt) cc_final: 0.8461 (mmm) REVERT: B 1043 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9196 (mm) REVERT: B 1053 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7908 (ttpp) REVERT: B 1065 ILE cc_start: 0.8291 (mm) cc_final: 0.8038 (mm) outliers start: 40 outliers final: 33 residues processed: 278 average time/residue: 0.2089 time to fit residues: 90.6879 Evaluate side-chains 280 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 54 optimal weight: 0.0000 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 115 optimal weight: 0.4980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 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 = 0.3969 r_free = 0.3969 target = 0.138354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114955 restraints weight = 28300.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116898 restraints weight = 19934.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.118656 restraints weight = 15187.142| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13307 Z= 0.204 Angle : 0.735 12.604 18051 Z= 0.363 Chirality : 0.046 0.356 2081 Planarity : 0.004 0.055 2240 Dihedral : 5.743 83.541 1777 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 23.28 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1651 helix: 1.27 (0.17), residues: 963 sheet: -1.35 (0.46), residues: 124 loop : -2.30 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.065 0.002 PHE B 659 TYR 0.025 0.001 TYR B 751 ARG 0.004 0.000 ARG A 653 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.82 seconds wall clock time: 54 minutes 17.51 seconds (3257.51 seconds total)