Starting phenix.real_space_refine on Sun Dec 29 06:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.map" model { file = "/net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox5_17257/12_2024/8ox5_17257.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6305 2.51 5 N 1609 2.21 5 O 1782 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9751 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 7008 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 20, 'TRANS': 848} Chain breaks: 4 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.65 Number of scatterers: 9751 At special positions: 0 Unit cell: (91.0976, 93.168, 166.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 47 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1782 8.00 N 1609 7.00 C 6305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 57.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.882A pdb=" N ASN A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.840A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.560A pdb=" N SER A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 172 Proline residue: A 147 - end of helix removed outlier: 3.782A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 355 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.594A pdb=" N ASN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.674A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.845A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 426 removed outlier: 3.526A pdb=" N TYR A 426 " --> pdb=" O LEU A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.541A pdb=" N LEU A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.583A pdb=" N ILE A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.679A pdb=" N PHE A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.733A pdb=" N ALA A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 removed outlier: 4.005A pdb=" N GLU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 673 " --> pdb=" O TRP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.678A pdb=" N GLU A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 737 through 746 removed outlier: 3.765A pdb=" N PHE A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 773 removed outlier: 3.640A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.562A pdb=" N ASN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 859 removed outlier: 3.687A pdb=" N GLU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.687A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 removed outlier: 3.599A pdb=" N LYS A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.641A pdb=" N MET A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 937 Processing helix chain 'A' and resid 938 through 971 removed outlier: 3.509A pdb=" N TRP A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.353A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1025 removed outlier: 3.612A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1057 removed outlier: 3.563A pdb=" N PHE A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) Proline residue: A1051 - end of helix removed outlier: 3.820A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1090 Processing helix chain 'A' and resid 1097 through 1119 removed outlier: 3.817A pdb=" N ASP A1116 " --> pdb=" O GLY A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.734A pdb=" N HIS A1123 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1180 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 46 through 59 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 60 through 74 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.593A pdb=" N SER B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 4.208A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 239 through 243 removed outlier: 4.117A pdb=" N MET B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 243' Processing helix chain 'B' and resid 250 through 253 removed outlier: 3.872A pdb=" N ILE B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.614A pdb=" N LEU B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.133A pdb=" N PHE A 466 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 707 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 604 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE A 593 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 606 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 591 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 730 through 732 removed outlier: 3.597A pdb=" N CYS A 865 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 866 " --> pdb=" O ILE A 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 889 through 892 removed outlier: 5.508A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 81 removed outlier: 4.140A pdb=" N ILE B 311 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.155A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1269 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: 3.02 Time building geometry restraints manager: 3.04 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: 3054 1.34 - 1.46: 2248 1.46 - 1.58: 4598 1.58 - 1.70: 5 1.70 - 1.82: 78 Bond restraints: 9983 Sorted by residual: bond pdb=" C3' ADP A1201 " pdb=" C4' ADP A1201 " ideal model delta sigma weight residual 1.524 1.282 0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1' ADP A1201 " pdb=" C2' ADP A1201 " ideal model delta sigma weight residual 1.524 1.287 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C4' ADP A1201 " pdb=" O4' ADP A1201 " ideal model delta sigma weight residual 1.426 1.565 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C6 ADP A1201 " pdb=" N6 ADP A1201 " ideal model delta sigma weight residual 1.355 1.490 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C2' ADP A1201 " pdb=" C3' ADP A1201 " ideal model delta sigma weight residual 1.524 1.652 -0.128 2.00e-02 2.50e+03 4.13e+01 ... (remaining 9978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.99: 13540 13.99 - 27.97: 4 27.97 - 41.96: 0 41.96 - 55.94: 0 55.94 - 69.93: 2 Bond angle restraints: 13546 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.61 -69.93 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.86 -69.23 3.00e+00 1.11e-01 5.33e+02 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 88.37 21.32 3.00e+00 1.11e-01 5.05e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.70 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 90.26 19.33 3.00e+00 1.11e-01 4.15e+01 ... (remaining 13541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5576 21.62 - 43.23: 319 43.23 - 64.85: 47 64.85 - 86.46: 16 86.46 - 108.08: 5 Dihedral angle restraints: 5963 sinusoidal: 2458 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual -86.00 -45.94 -40.06 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA TYR B 121 " pdb=" C TYR B 121 " pdb=" N TYR B 122 " pdb=" CA TYR B 122 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU A 692 " pdb=" C GLU A 692 " pdb=" N GLU A 693 " pdb=" CA GLU A 693 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1326 0.062 - 0.123: 178 0.123 - 0.185: 19 0.185 - 0.247: 0 0.247 - 0.308: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CG LEU A1027 " pdb=" CB LEU A1027 " pdb=" CD1 LEU A1027 " pdb=" CD2 LEU A1027 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE A 985 " pdb=" CA ILE A 985 " pdb=" CG1 ILE A 985 " pdb=" CG2 ILE A 985 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 1522 not shown) Planarity restraints: 1700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 96 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 97 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 455 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LYS A 455 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A 455 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 456 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 132 " -0.135 9.50e-02 1.11e+02 6.09e-02 2.79e+00 pdb=" NE ARG B 132 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 132 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 132 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 132 " -0.001 2.00e-02 2.50e+03 ... (remaining 1697 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 18 2.12 - 2.82: 3035 2.82 - 3.51: 14644 3.51 - 4.21: 24131 4.21 - 4.90: 42647 Nonbonded interactions: 84475 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" F4 ALF A1202 " model vdw 1.430 2.990 nonbonded pdb=" OD2 ASP A 893 " pdb=" OE2 GLU A 914 " model vdw 1.440 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1203 " model vdw 1.454 2.170 nonbonded pdb=" OD1 ASP A 454 " pdb="AL ALF A1202 " model vdw 1.818 2.760 nonbonded pdb=" F1 ALF A1202 " pdb="MG MG A1203 " model vdw 1.872 2.120 ... (remaining 84470 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=1.00 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: 1.050 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 25.910 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 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 0.242 9983 Z= 0.406 Angle : 1.127 69.927 13546 Z= 0.443 Chirality : 0.043 0.308 1525 Planarity : 0.005 0.061 1697 Dihedral : 14.359 108.081 3698 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.86 (0.23), residues: 1185 helix: -0.90 (0.22), residues: 541 sheet: -0.53 (0.47), residues: 135 loop : -1.70 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 805 HIS 0.008 0.001 HIS B 131 PHE 0.016 0.001 PHE B 108 TYR 0.026 0.002 TYR A 992 ARG 0.013 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 1144 TYR cc_start: 0.7649 (m-80) cc_final: 0.7421 (m-10) REVERT: B 121 TYR cc_start: 0.6083 (m-10) cc_final: 0.5736 (m-10) REVERT: B 132 ARG cc_start: 0.4478 (ttp80) cc_final: 0.3151 (ttp80) REVERT: B 244 ASP cc_start: 0.4249 (t70) cc_final: 0.4016 (m-30) REVERT: B 262 ARG cc_start: 0.7581 (ttt90) cc_final: 0.6538 (ttp80) outliers start: 0 outliers final: 1 residues processed: 153 average time/residue: 0.9260 time to fit residues: 155.6624 Evaluate side-chains 120 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN B 129 GLN B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9983 Z= 0.261 Angle : 0.911 32.570 13546 Z= 0.411 Chirality : 0.046 0.225 1525 Planarity : 0.005 0.038 1697 Dihedral : 8.150 71.848 1422 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.15 % Allowed : 9.64 % Favored : 89.22 % 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: -1.68 (0.24), residues: 1185 helix: -0.68 (0.20), residues: 609 sheet: -0.59 (0.45), residues: 149 loop : -1.78 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 669 HIS 0.006 0.001 HIS A 905 PHE 0.018 0.002 PHE A 124 TYR 0.018 0.002 TYR A 992 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.074 Fit side-chains REVERT: B 262 ARG cc_start: 0.7487 (ttt90) cc_final: 0.6346 (ttp80) REVERT: B 274 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6329 (mtt-85) outliers start: 12 outliers final: 2 residues processed: 133 average time/residue: 0.9260 time to fit residues: 135.9662 Evaluate side-chains 107 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9983 Z= 0.275 Angle : 0.872 30.647 13546 Z= 0.389 Chirality : 0.045 0.221 1525 Planarity : 0.005 0.059 1697 Dihedral : 6.760 55.167 1422 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.19 % Allowed : 12.60 % Favored : 85.21 % 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: -1.78 (0.23), residues: 1185 helix: -0.73 (0.20), residues: 619 sheet: -0.63 (0.46), residues: 144 loop : -1.87 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 669 HIS 0.008 0.001 HIS A 535 PHE 0.013 0.002 PHE A 113 TYR 0.035 0.002 TYR A 944 ARG 0.009 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.059 Fit side-chains REVERT: A 425 MET cc_start: 0.7344 (mtm) cc_final: 0.7106 (mtm) REVERT: A 530 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5203 (pp) REVERT: A 603 MET cc_start: 0.6814 (ttp) cc_final: 0.6517 (ttt) REVERT: A 1147 LEU cc_start: 0.7546 (tp) cc_final: 0.7286 (mt) REVERT: B 244 ASP cc_start: 0.4603 (t70) cc_final: 0.4313 (m-30) REVERT: B 262 ARG cc_start: 0.7794 (ttt90) cc_final: 0.6488 (ttp80) REVERT: B 274 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6366 (mtt-85) outliers start: 23 outliers final: 7 residues processed: 139 average time/residue: 0.8361 time to fit residues: 129.3500 Evaluate side-chains 121 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9983 Z= 0.245 Angle : 0.864 31.635 13546 Z= 0.378 Chirality : 0.044 0.235 1525 Planarity : 0.004 0.039 1697 Dihedral : 6.107 56.132 1422 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.00 % Allowed : 15.94 % Favored : 82.06 % 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: -1.70 (0.23), residues: 1185 helix: -0.65 (0.20), residues: 617 sheet: -0.42 (0.47), residues: 133 loop : -1.91 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 669 HIS 0.011 0.001 HIS A 535 PHE 0.028 0.002 PHE A 966 TYR 0.026 0.002 TYR A 944 ARG 0.004 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.072 Fit side-chains REVERT: A 530 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5242 (pp) REVERT: A 603 MET cc_start: 0.6798 (ttp) cc_final: 0.6450 (ttt) REVERT: A 673 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6234 (t80) REVERT: A 1147 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7182 (mt) REVERT: B 244 ASP cc_start: 0.4643 (t70) cc_final: 0.4247 (m-30) REVERT: B 262 ARG cc_start: 0.7819 (ttt90) cc_final: 0.6490 (ttp80) outliers start: 21 outliers final: 9 residues processed: 135 average time/residue: 0.8410 time to fit residues: 126.1548 Evaluate side-chains 119 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 449 HIS A 630 HIS A 633 ASN A 958 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9983 Z= 0.225 Angle : 0.852 31.713 13546 Z= 0.371 Chirality : 0.043 0.241 1525 Planarity : 0.004 0.050 1697 Dihedral : 5.837 55.676 1422 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.10 % Allowed : 16.89 % Favored : 81.01 % 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: -1.55 (0.24), residues: 1185 helix: -0.46 (0.20), residues: 612 sheet: -0.96 (0.43), residues: 148 loop : -1.73 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 729 HIS 0.007 0.001 HIS A 905 PHE 0.029 0.001 PHE A 966 TYR 0.025 0.002 TYR A 944 ARG 0.005 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.143 Fit side-chains REVERT: A 530 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5199 (pp) REVERT: A 603 MET cc_start: 0.6659 (ttp) cc_final: 0.6426 (ttt) REVERT: A 673 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6330 (t80) REVERT: A 769 MET cc_start: 0.2124 (tpt) cc_final: 0.1067 (tpp) REVERT: A 1147 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7314 (mp) REVERT: B 244 ASP cc_start: 0.4659 (t70) cc_final: 0.4206 (m-30) outliers start: 22 outliers final: 8 residues processed: 139 average time/residue: 0.7856 time to fit residues: 122.7107 Evaluate side-chains 120 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS A 633 ASN A 989 ASN A1070 GLN A1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9983 Z= 0.219 Angle : 0.854 31.616 13546 Z= 0.370 Chirality : 0.044 0.262 1525 Planarity : 0.004 0.059 1697 Dihedral : 5.757 56.240 1422 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.72 % Allowed : 19.08 % Favored : 79.20 % 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: -1.45 (0.24), residues: 1185 helix: -0.38 (0.20), residues: 610 sheet: -0.69 (0.46), residues: 137 loop : -1.75 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 207 HIS 0.007 0.001 HIS A 905 PHE 0.030 0.001 PHE A 966 TYR 0.022 0.002 TYR A 944 ARG 0.007 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.065 Fit side-chains REVERT: A 603 MET cc_start: 0.6669 (ttp) cc_final: 0.6384 (ttt) REVERT: A 673 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6259 (t80) REVERT: A 674 MET cc_start: 0.7205 (mmm) cc_final: 0.6992 (mmt) REVERT: B 244 ASP cc_start: 0.4749 (t70) cc_final: 0.4341 (m-30) outliers start: 18 outliers final: 8 residues processed: 128 average time/residue: 0.8426 time to fit residues: 120.6775 Evaluate side-chains 114 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 989 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9983 Z= 0.212 Angle : 0.864 31.704 13546 Z= 0.374 Chirality : 0.043 0.267 1525 Planarity : 0.004 0.058 1697 Dihedral : 5.619 56.071 1420 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.72 % Allowed : 19.75 % Favored : 78.53 % 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: -1.38 (0.24), residues: 1185 helix: -0.29 (0.21), residues: 611 sheet: -0.77 (0.46), residues: 137 loop : -1.73 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 729 HIS 0.014 0.001 HIS A 535 PHE 0.031 0.002 PHE A 124 TYR 0.021 0.001 TYR A 944 ARG 0.008 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.070 Fit side-chains REVERT: A 595 ASP cc_start: 0.5274 (OUTLIER) cc_final: 0.4603 (t0) REVERT: A 603 MET cc_start: 0.6771 (ttp) cc_final: 0.6455 (ttt) REVERT: A 673 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6287 (t80) REVERT: B 174 ILE cc_start: 0.4751 (OUTLIER) cc_final: 0.4452 (mt) REVERT: B 244 ASP cc_start: 0.4755 (t70) cc_final: 0.4333 (m-30) outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.8405 time to fit residues: 121.6309 Evaluate side-chains 115 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 0.0000 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9983 Z= 0.198 Angle : 0.862 31.595 13546 Z= 0.374 Chirality : 0.044 0.289 1525 Planarity : 0.004 0.059 1697 Dihedral : 5.565 56.051 1420 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.15 % Allowed : 20.80 % Favored : 78.05 % 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: -1.30 (0.24), residues: 1185 helix: -0.25 (0.21), residues: 613 sheet: -0.88 (0.46), residues: 137 loop : -1.59 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 729 HIS 0.006 0.001 HIS A 905 PHE 0.028 0.001 PHE A 966 TYR 0.020 0.001 TYR A 944 ARG 0.007 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.947 Fit side-chains REVERT: A 595 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4533 (t0) REVERT: A 603 MET cc_start: 0.6672 (ttp) cc_final: 0.6451 (ttt) REVERT: A 673 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6210 (t80) REVERT: B 174 ILE cc_start: 0.4727 (OUTLIER) cc_final: 0.4471 (mt) REVERT: B 244 ASP cc_start: 0.4784 (t70) cc_final: 0.4304 (m-30) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.7530 time to fit residues: 94.9723 Evaluate side-chains 106 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.0570 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9983 Z= 0.199 Angle : 0.866 31.633 13546 Z= 0.371 Chirality : 0.044 0.271 1525 Planarity : 0.004 0.052 1697 Dihedral : 5.527 56.175 1420 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.24 % Allowed : 21.47 % Favored : 77.29 % 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: -1.36 (0.24), residues: 1185 helix: -0.25 (0.21), residues: 619 sheet: -1.15 (0.43), residues: 148 loop : -1.64 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 729 HIS 0.006 0.001 HIS A 905 PHE 0.026 0.002 PHE A 966 TYR 0.018 0.001 TYR A 944 ARG 0.009 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 595 ASP cc_start: 0.5156 (OUTLIER) cc_final: 0.4519 (t0) REVERT: A 603 MET cc_start: 0.6694 (ttp) cc_final: 0.6383 (ttt) REVERT: A 673 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6205 (t80) REVERT: B 174 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4449 (mt) REVERT: B 244 ASP cc_start: 0.4810 (t70) cc_final: 0.4336 (m-30) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.7947 time to fit residues: 107.1683 Evaluate side-chains 110 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 648 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9983 Z= 0.213 Angle : 0.882 31.993 13546 Z= 0.379 Chirality : 0.045 0.302 1525 Planarity : 0.004 0.057 1697 Dihedral : 5.550 56.168 1420 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.05 % Allowed : 21.85 % Favored : 77.10 % 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: -1.30 (0.24), residues: 1185 helix: -0.23 (0.21), residues: 614 sheet: -1.15 (0.43), residues: 147 loop : -1.53 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.006 0.001 HIS A 905 PHE 0.026 0.001 PHE A 966 TYR 0.015 0.001 TYR A 944 ARG 0.009 0.000 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 595 ASP cc_start: 0.5176 (OUTLIER) cc_final: 0.4534 (t0) REVERT: A 673 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 174 ILE cc_start: 0.4772 (OUTLIER) cc_final: 0.4484 (mt) REVERT: B 244 ASP cc_start: 0.4793 (t70) cc_final: 0.4385 (m-30) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.7035 time to fit residues: 90.6154 Evaluate side-chains 109 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.241833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.196662 restraints weight = 10161.463| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.20 r_work: 0.4270 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9983 Z= 0.278 Angle : 0.914 32.366 13546 Z= 0.397 Chirality : 0.047 0.333 1525 Planarity : 0.004 0.058 1697 Dihedral : 5.698 56.567 1420 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.34 % Allowed : 21.95 % Favored : 76.72 % 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: -1.48 (0.24), residues: 1185 helix: -0.40 (0.20), residues: 614 sheet: -1.10 (0.43), residues: 147 loop : -1.62 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 669 HIS 0.007 0.001 HIS A 905 PHE 0.021 0.002 PHE A 950 TYR 0.017 0.002 TYR A 944 ARG 0.010 0.001 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.00 seconds wall clock time: 55 minutes 35.68 seconds (3335.68 seconds total)