Starting phenix.real_space_refine on Tue Jun 17 01:08:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.map" model { file = "/net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gz1_51719/06_2025/9gz1_51719.cif" } resolution = 3.7 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= 0.002 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 12246 2.51 5 N 3263 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19295 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7296 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 31, 'TRANS': 868} Chain breaks: 2 Chain: "B" Number of atoms: 7296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7296 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 31, 'TRANS': 868} Chain breaks: 2 Chain: "C" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1131 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "E" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1157 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "D" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1148 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "F" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1159 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.12, per 1000 atoms: 0.63 Number of scatterers: 19295 At special positions: 0 Unit cell: (94.53, 156.18, 172.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 6 15.00 Mg 4 11.99 O 3662 8.00 N 3263 7.00 C 12246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4482 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 65.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.627A pdb=" N ALA A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.105A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.740A pdb=" N ALA A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.714A pdb=" N ILE A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.699A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.845A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.940A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.635A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 removed outlier: 4.048A pdb=" N ASP A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.896A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.552A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 444 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.533A pdb=" N ASN A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.557A pdb=" N GLU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 708 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 737 through 749 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 766 through 826 removed outlier: 3.987A pdb=" N ARG A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.630A pdb=" N TYR A 833 " --> pdb=" O TRP A 829 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 840 through 932 removed outlier: 3.609A pdb=" N GLU A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.589A pdb=" N ALA B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 8 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Proline residue: B 14 - end of helix Processing helix chain 'B' and resid 19 through 27 removed outlier: 3.963A pdb=" N GLN B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.608A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 4.096A pdb=" N VAL B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 202 Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.932A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.994A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 283 through 293 removed outlier: 4.256A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 306 through 309 removed outlier: 3.877A pdb=" N ASP B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.073A pdb=" N GLN B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.861A pdb=" N LEU B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.539A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 444 removed outlier: 3.801A pdb=" N TYR B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 495 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.523A pdb=" N ILE B 524 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 538 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.578A pdb=" N PHE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.541A pdb=" N GLN B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 737 through 749 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 768 through 825 removed outlier: 3.900A pdb=" N LEU B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 836 removed outlier: 4.040A pdb=" N LEU B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 932 removed outlier: 3.601A pdb=" N GLN B 892 " --> pdb=" O GLN B 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.603A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.730A pdb=" N PHE C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 157 through 166 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'E' and resid 41 through 56 removed outlier: 3.785A pdb=" N GLU E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.636A pdb=" N ARG E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 92 through 99 Processing helix chain 'E' and resid 102 through 115 Proline residue: E 108 - end of helix removed outlier: 3.703A pdb=" N GLN E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.717A pdb=" N GLY E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 152 removed outlier: 3.956A pdb=" N HIS E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.539A pdb=" N VAL E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 187 removed outlier: 3.694A pdb=" N SER E 186 " --> pdb=" O LYS E 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.760A pdb=" N LYS D 62 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 removed outlier: 3.669A pdb=" N ALA D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 73 " --> pdb=" O MET D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.632A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.674A pdb=" N ILE D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.606A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 4.480A pdb=" N MET F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 29 Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 48 through 57 removed outlier: 4.027A pdb=" N ALA F 54 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.844A pdb=" N LEU F 83 " --> pdb=" O PHE F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 94 removed outlier: 3.687A pdb=" N ASP F 94 " --> pdb=" O LYS F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 91 through 94' Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.795A pdb=" N THR F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 4.262A pdb=" N THR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 142 removed outlier: 3.725A pdb=" N PHE F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 removed outlier: 7.067A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 77 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.807A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY A 245 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.866A pdb=" N SER A 241 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 removed outlier: 3.689A pdb=" N GLU A 409 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 removed outlier: 4.424A pdb=" N GLN A 564 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 578 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 4.429A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 765 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 713 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 72 removed outlier: 3.724A pdb=" N VAL B 71 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 59 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG B 54 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 52 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.588A pdb=" N PHE B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 455 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 406 Processing sheet with id=AB4, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AB6, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB7, first strand: chain 'E' and resid 139 through 141 1089 hydrogen bonds defined for protein. 3162 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: 7.01 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4070 1.33 - 1.45: 4296 1.45 - 1.57: 11077 1.57 - 1.69: 6 1.69 - 1.81: 202 Bond restraints: 19651 Sorted by residual: bond pdb=" C07 XB2 A1204 " pdb=" N03 XB2 A1204 " ideal model delta sigma weight residual 1.425 1.361 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C GLY E 59 " pdb=" N GLU E 60 " ideal model delta sigma weight residual 1.332 1.371 -0.038 1.40e-02 5.10e+03 7.46e+00 bond pdb=" CZ ARG A 712 " pdb=" NH2 ARG A 712 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.14e+00 bond pdb=" C07 XB2 B1204 " pdb=" N03 XB2 B1204 " ideal model delta sigma weight residual 1.425 1.372 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CZ ARG B 739 " pdb=" NH2 ARG B 739 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.69e+00 ... (remaining 19646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 25432 2.63 - 5.27: 874 5.27 - 7.90: 113 7.90 - 10.54: 18 10.54 - 13.17: 8 Bond angle restraints: 26445 Sorted by residual: angle pdb=" N CYS E 61 " pdb=" CA CYS E 61 " pdb=" C CYS E 61 " ideal model delta sigma weight residual 112.93 121.21 -8.28 1.12e+00 7.97e-01 5.47e+01 angle pdb=" N LYS A 912 " pdb=" CA LYS A 912 " pdb=" CB LYS A 912 " ideal model delta sigma weight residual 110.01 119.88 -9.87 1.45e+00 4.76e-01 4.63e+01 angle pdb=" CA ASP A 382 " pdb=" CB ASP A 382 " pdb=" CG ASP A 382 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.00e+00 1.00e+00 3.95e+01 angle pdb=" N ASP F 94 " pdb=" CA ASP F 94 " pdb=" C ASP F 94 " ideal model delta sigma weight residual 113.57 121.29 -7.72 1.38e+00 5.25e-01 3.13e+01 angle pdb=" C TRP B 130 " pdb=" N LEU B 131 " pdb=" CA LEU B 131 " ideal model delta sigma weight residual 122.31 134.99 -12.68 2.34e+00 1.83e-01 2.93e+01 ... (remaining 26440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 11271 23.38 - 46.75: 581 46.75 - 70.13: 99 70.13 - 93.51: 29 93.51 - 116.88: 2 Dihedral angle restraints: 11982 sinusoidal: 5053 harmonic: 6929 Sorted by residual: dihedral pdb=" O1B ADP A1202 " pdb=" O3A ADP A1202 " pdb=" PB ADP A1202 " pdb=" PA ADP A1202 " ideal model delta sinusoidal sigma weight residual -60.00 -176.89 116.88 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" CA LYS E 62 " pdb=" C LYS E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C5' ADP A1202 " pdb=" O5' ADP A1202 " pdb=" PA ADP A1202 " pdb=" O2A ADP A1202 " ideal model delta sinusoidal sigma weight residual -60.00 55.04 -115.04 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 11979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2355 0.078 - 0.157: 435 0.157 - 0.235: 47 0.235 - 0.313: 13 0.313 - 0.392: 6 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA LYS A 912 " pdb=" N LYS A 912 " pdb=" C LYS A 912 " pdb=" CB LYS A 912 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB THR B 135 " pdb=" CA THR B 135 " pdb=" OG1 THR B 135 " pdb=" CG2 THR B 135 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CG LEU A 770 " pdb=" CB LEU A 770 " pdb=" CD1 LEU A 770 " pdb=" CD2 LEU A 770 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2853 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 XB2 B1204 " -0.037 2.00e-02 2.50e+03 1.02e-01 2.87e+02 pdb=" C04 XB2 B1204 " 0.245 2.00e-02 2.50e+03 pdb=" C07 XB2 B1204 " -0.045 2.00e-02 2.50e+03 pdb=" C08 XB2 B1204 " -0.028 2.00e-02 2.50e+03 pdb=" C09 XB2 B1204 " 0.026 2.00e-02 2.50e+03 pdb=" C11 XB2 B1204 " 0.070 2.00e-02 2.50e+03 pdb=" N03 XB2 B1204 " 0.036 2.00e-02 2.50e+03 pdb=" N10 XB2 B1204 " 0.003 2.00e-02 2.50e+03 pdb=" N19 XB2 B1204 " 0.024 2.00e-02 2.50e+03 pdb=" O01 XB2 B1204 " -0.150 2.00e-02 2.50e+03 pdb=" O20 XB2 B1204 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 XB2 A1204 " -0.020 2.00e-02 2.50e+03 5.02e-02 6.93e+01 pdb=" C04 XB2 A1204 " 0.081 2.00e-02 2.50e+03 pdb=" C07 XB2 A1204 " -0.020 2.00e-02 2.50e+03 pdb=" C08 XB2 A1204 " -0.092 2.00e-02 2.50e+03 pdb=" C09 XB2 A1204 " -0.049 2.00e-02 2.50e+03 pdb=" C11 XB2 A1204 " 0.076 2.00e-02 2.50e+03 pdb=" N03 XB2 A1204 " -0.014 2.00e-02 2.50e+03 pdb=" N10 XB2 A1204 " 0.037 2.00e-02 2.50e+03 pdb=" N19 XB2 A1204 " -0.038 2.00e-02 2.50e+03 pdb=" O01 XB2 A1204 " 0.015 2.00e-02 2.50e+03 pdb=" O20 XB2 A1204 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 164 " 0.001 2.00e-02 2.50e+03 5.83e-02 6.80e+01 pdb=" CG TYR A 164 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 164 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 164 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 164 " -0.108 2.00e-02 2.50e+03 pdb=" CZ TYR A 164 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 164 " 0.067 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 14 2.45 - 3.06: 13260 3.06 - 3.67: 31097 3.67 - 4.29: 44659 4.29 - 4.90: 71733 Nonbonded interactions: 160763 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O2B ADP A1202 " model vdw 1.835 2.170 nonbonded pdb=" OG1 THR B 185 " pdb="MG MG B1201 " model vdw 1.843 2.170 nonbonded pdb="MG MG A1201 " pdb=" O1 PO4 A1203 " model vdw 1.863 2.170 nonbonded pdb=" OG1 THR A 185 " pdb="MG MG A1201 " model vdw 1.872 2.170 nonbonded pdb="MG MG B1201 " pdb=" O2B ADP B1202 " model vdw 1.898 2.170 ... (remaining 160758 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'E' and resid 43 through 187) } ncs_group { reference = (chain 'D' and (resid 18 through 160 or resid 201)) selection = (chain 'F' and (resid 18 through 160 or resid 201)) } 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 46.460 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 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 : 0.008 0.785 19652 Z= 0.622 Angle : 1.124 13.174 26445 Z= 0.656 Chirality : 0.064 0.392 2856 Planarity : 0.012 0.227 3436 Dihedral : 14.683 116.883 7500 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.09 % 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: -1.83 (0.15), residues: 2363 helix: -1.09 (0.12), residues: 1320 sheet: -0.80 (0.38), residues: 179 loop : -1.23 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP B 829 HIS 0.012 0.002 HIS A 668 PHE 0.052 0.003 PHE B 821 TYR 0.108 0.007 TYR A 164 ARG 0.043 0.004 ARG B 845 Details of bonding type rmsd hydrogen bonds : bond 0.14076 ( 1089) hydrogen bonds : angle 7.16579 ( 3162) covalent geometry : bond 0.00535 (19651) covalent geometry : angle 1.12376 (26445) Misc. bond : bond 0.78492 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5591 (mmm) cc_final: 0.5351 (mmm) REVERT: A 215 THR cc_start: 0.7796 (p) cc_final: 0.7507 (t) REVERT: A 240 ASN cc_start: 0.7571 (t0) cc_final: 0.7301 (t0) REVERT: A 397 LYS cc_start: 0.8034 (mttt) cc_final: 0.7680 (mptt) REVERT: A 499 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 500 GLU cc_start: 0.6531 (tt0) cc_final: 0.6243 (mt-10) REVERT: A 608 LEU cc_start: 0.8024 (tp) cc_final: 0.7752 (tt) REVERT: A 685 ASP cc_start: 0.7432 (m-30) cc_final: 0.6879 (m-30) REVERT: A 785 ILE cc_start: 0.8334 (tt) cc_final: 0.8062 (mp) REVERT: A 786 THR cc_start: 0.7860 (m) cc_final: 0.7249 (m) REVERT: A 789 GLN cc_start: 0.7800 (mt0) cc_final: 0.7514 (mt0) REVERT: A 799 MET cc_start: 0.7279 (mmt) cc_final: 0.6678 (mmt) REVERT: A 802 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7871 (mmtm) REVERT: A 804 LEU cc_start: 0.8600 (mm) cc_final: 0.7913 (mm) REVERT: A 806 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 812 LEU cc_start: 0.8323 (mt) cc_final: 0.7706 (mt) REVERT: A 822 MET cc_start: 0.6317 (ppp) cc_final: 0.6048 (ppp) REVERT: A 852 MET cc_start: 0.7805 (tmm) cc_final: 0.7385 (tmm) REVERT: B 149 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7451 (mp0) REVERT: B 169 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6903 (ttm110) REVERT: B 179 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 232 ASN cc_start: 0.7386 (m-40) cc_final: 0.7016 (m-40) REVERT: B 264 GLU cc_start: 0.6941 (tt0) cc_final: 0.6631 (tt0) REVERT: B 266 TYR cc_start: 0.6820 (m-80) cc_final: 0.6464 (m-80) REVERT: B 429 LYS cc_start: 0.8506 (mttt) cc_final: 0.7953 (mtpp) REVERT: B 448 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 457 ILE cc_start: 0.6907 (mt) cc_final: 0.5365 (tt) REVERT: B 475 GLN cc_start: 0.7267 (mm-40) cc_final: 0.7042 (mm-40) REVERT: B 478 ILE cc_start: 0.8331 (pt) cc_final: 0.8026 (tt) REVERT: B 484 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7373 (mmmm) REVERT: B 515 MET cc_start: 0.5031 (mmm) cc_final: 0.4801 (mmm) REVERT: B 539 MET cc_start: 0.6328 (mtt) cc_final: 0.5943 (mtt) REVERT: B 659 MET cc_start: 0.7161 (mtp) cc_final: 0.6550 (mtp) REVERT: B 686 ASN cc_start: 0.7226 (m-40) cc_final: 0.6974 (m-40) REVERT: B 734 GLN cc_start: 0.6885 (mp10) cc_final: 0.6395 (mp10) REVERT: B 800 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 819 ARG cc_start: 0.8075 (tpt170) cc_final: 0.7603 (tpt90) REVERT: B 860 LYS cc_start: 0.8881 (tppt) cc_final: 0.8267 (tppt) REVERT: B 861 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 96 MET cc_start: 0.7557 (ttp) cc_final: 0.7126 (tmm) REVERT: C 110 MET cc_start: 0.7548 (ttp) cc_final: 0.7032 (ttp) REVERT: C 111 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 125 PHE cc_start: 0.7674 (m-80) cc_final: 0.7027 (m-80) REVERT: C 156 MET cc_start: 0.5506 (mmt) cc_final: 0.4783 (mmt) REVERT: C 164 LEU cc_start: 0.8189 (tt) cc_final: 0.7969 (tt) REVERT: E 95 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 96 MET cc_start: 0.8045 (ttm) cc_final: 0.7495 (ttm) REVERT: E 124 ASP cc_start: 0.7031 (t0) cc_final: 0.6651 (t0) REVERT: E 125 PHE cc_start: 0.7129 (m-10) cc_final: 0.6817 (m-10) REVERT: E 176 ASN cc_start: 0.8303 (t0) cc_final: 0.7998 (t0) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3415 time to fit residues: 231.3405 Evaluate side-chains 387 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 184 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.208534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.175515 restraints weight = 39091.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180891 restraints weight = 21951.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.184551 restraints weight = 13941.032| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19652 Z= 0.195 Angle : 0.763 9.163 26445 Z= 0.399 Chirality : 0.048 0.187 2856 Planarity : 0.005 0.102 3436 Dihedral : 7.541 102.332 2599 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.16 % Allowed : 8.87 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.17), residues: 2363 helix: 0.07 (0.13), residues: 1359 sheet: -0.78 (0.39), residues: 162 loop : -0.65 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 829 HIS 0.006 0.001 HIS A 492 PHE 0.027 0.002 PHE D 21 TYR 0.028 0.002 TYR A 722 ARG 0.007 0.001 ARG B 870 Details of bonding type rmsd hydrogen bonds : bond 0.05583 ( 1089) hydrogen bonds : angle 5.83842 ( 3162) covalent geometry : bond 0.00421 (19651) covalent geometry : angle 0.76304 (26445) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 399 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7800 (tp30) cc_final: 0.7354 (tm-30) REVERT: A 195 PHE cc_start: 0.6734 (m-80) cc_final: 0.6420 (m-80) REVERT: A 215 THR cc_start: 0.7864 (p) cc_final: 0.7621 (t) REVERT: A 224 ASN cc_start: 0.6301 (m-40) cc_final: 0.6005 (t0) REVERT: A 240 ASN cc_start: 0.7668 (t0) cc_final: 0.7396 (t0) REVERT: A 241 SER cc_start: 0.8472 (t) cc_final: 0.8168 (p) REVERT: A 397 LYS cc_start: 0.8013 (mttt) cc_final: 0.7703 (mptt) REVERT: A 433 GLU cc_start: 0.6108 (tm-30) cc_final: 0.5746 (tm-30) REVERT: A 493 MET cc_start: 0.7153 (mmt) cc_final: 0.6744 (mpp) REVERT: A 499 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 500 GLU cc_start: 0.6644 (tt0) cc_final: 0.6183 (mt-10) REVERT: A 562 ASN cc_start: 0.5993 (m110) cc_final: 0.5706 (m110) REVERT: A 608 LEU cc_start: 0.7968 (tp) cc_final: 0.7748 (tt) REVERT: A 685 ASP cc_start: 0.7388 (m-30) cc_final: 0.6907 (m-30) REVERT: A 690 MET cc_start: 0.5355 (ttt) cc_final: 0.4647 (ttt) REVERT: A 709 PHE cc_start: 0.6932 (m-80) cc_final: 0.6634 (m-80) REVERT: A 799 MET cc_start: 0.7355 (mmt) cc_final: 0.6778 (mmt) REVERT: A 804 LEU cc_start: 0.8629 (mm) cc_final: 0.8315 (mm) REVERT: A 822 MET cc_start: 0.6358 (ppp) cc_final: 0.5948 (ppp) REVERT: A 845 ARG cc_start: 0.7371 (tpp-160) cc_final: 0.6954 (tpp-160) REVERT: A 852 MET cc_start: 0.8104 (tmm) cc_final: 0.7584 (tmm) REVERT: B 129 LYS cc_start: 0.8149 (tttt) cc_final: 0.7661 (ttpt) REVERT: B 149 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7312 (mp0) REVERT: B 179 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 232 ASN cc_start: 0.7184 (m-40) cc_final: 0.6903 (m-40) REVERT: B 266 TYR cc_start: 0.6707 (m-80) cc_final: 0.6489 (m-80) REVERT: B 269 GLU cc_start: 0.6260 (tt0) cc_final: 0.5893 (tt0) REVERT: B 293 LYS cc_start: 0.8304 (ptmt) cc_final: 0.8008 (pttm) REVERT: B 330 MET cc_start: 0.6441 (mpp) cc_final: 0.5976 (mpp) REVERT: B 484 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7492 (mmmm) REVERT: B 659 MET cc_start: 0.7140 (mtp) cc_final: 0.6587 (mtp) REVERT: B 700 GLU cc_start: 0.7285 (mp0) cc_final: 0.7055 (mp0) REVERT: B 734 GLN cc_start: 0.6906 (mp10) cc_final: 0.6639 (mp10) REVERT: B 740 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7764 (mtmm) REVERT: B 800 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 819 ARG cc_start: 0.8031 (tpt170) cc_final: 0.7279 (mmm160) REVERT: B 830 MET cc_start: 0.6061 (pp-130) cc_final: 0.5819 (ppp) REVERT: B 860 LYS cc_start: 0.8883 (tppt) cc_final: 0.8171 (tppt) REVERT: B 861 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 872 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 922 MET cc_start: 0.6914 (mmm) cc_final: 0.6691 (mmm) REVERT: C 64 THR cc_start: 0.7900 (t) cc_final: 0.7522 (p) REVERT: C 96 MET cc_start: 0.7575 (ttp) cc_final: 0.7144 (tmm) REVERT: C 125 PHE cc_start: 0.7663 (m-80) cc_final: 0.7003 (m-80) REVERT: E 65 LEU cc_start: 0.7284 (tp) cc_final: 0.6965 (tt) REVERT: E 95 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8093 (mt-10) REVERT: E 96 MET cc_start: 0.8164 (ttm) cc_final: 0.7547 (ttm) REVERT: E 124 ASP cc_start: 0.7090 (t0) cc_final: 0.6694 (t0) REVERT: E 125 PHE cc_start: 0.7095 (m-10) cc_final: 0.6737 (m-10) REVERT: D 20 MET cc_start: 0.2917 (pmm) cc_final: 0.2061 (ppp) REVERT: D 56 MET cc_start: 0.6912 (ttm) cc_final: 0.6679 (ttt) REVERT: D 138 MET cc_start: 0.7707 (tpp) cc_final: 0.7164 (mmm) outliers start: 24 outliers final: 12 residues processed: 406 average time/residue: 0.3384 time to fit residues: 206.2114 Evaluate side-chains 384 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 372 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain F residue 69 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 160 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 482 ASN B 486 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.208313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.175564 restraints weight = 38834.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.180959 restraints weight = 21945.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.184666 restraints weight = 13881.060| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19652 Z= 0.164 Angle : 0.686 10.090 26445 Z= 0.356 Chirality : 0.044 0.184 2856 Planarity : 0.004 0.089 3436 Dihedral : 7.237 105.127 2599 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.83 % Allowed : 12.10 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.18 (0.17), residues: 2363 helix: 0.35 (0.13), residues: 1353 sheet: -0.52 (0.41), residues: 157 loop : -0.61 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.040 0.002 PHE E 55 TYR 0.025 0.002 TYR A 722 ARG 0.005 0.000 ARG B 870 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 1089) hydrogen bonds : angle 5.53515 ( 3162) covalent geometry : bond 0.00351 (19651) covalent geometry : angle 0.68562 (26445) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 384 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 98 GLU cc_start: 0.7563 (tp30) cc_final: 0.7272 (tm-30) REVERT: A 195 PHE cc_start: 0.6696 (m-80) cc_final: 0.6172 (m-80) REVERT: A 240 ASN cc_start: 0.7723 (t0) cc_final: 0.7376 (t0) REVERT: A 241 SER cc_start: 0.8450 (t) cc_final: 0.8008 (p) REVERT: A 397 LYS cc_start: 0.7950 (mttt) cc_final: 0.7670 (mptt) REVERT: A 433 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5649 (tm-30) REVERT: A 499 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6812 (tp30) REVERT: A 500 GLU cc_start: 0.6618 (tt0) cc_final: 0.6197 (mt-10) REVERT: A 551 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7864 (mmmt) REVERT: A 562 ASN cc_start: 0.6073 (m110) cc_final: 0.5718 (m110) REVERT: A 589 ASN cc_start: 0.6409 (t0) cc_final: 0.6000 (t0) REVERT: A 608 LEU cc_start: 0.7911 (tp) cc_final: 0.7710 (tt) REVERT: A 690 MET cc_start: 0.5444 (ttt) cc_final: 0.4216 (ttt) REVERT: A 799 MET cc_start: 0.7404 (mmt) cc_final: 0.6678 (mmt) REVERT: A 822 MET cc_start: 0.6352 (ppp) cc_final: 0.5889 (ppp) REVERT: A 845 ARG cc_start: 0.7234 (tpp-160) cc_final: 0.6846 (tpp-160) REVERT: A 852 MET cc_start: 0.8058 (tmm) cc_final: 0.7496 (tmm) REVERT: B 129 LYS cc_start: 0.8135 (tttt) cc_final: 0.7651 (ttpt) REVERT: B 133 VAL cc_start: 0.8100 (p) cc_final: 0.7610 (t) REVERT: B 179 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6879 (mt-10) REVERT: B 232 ASN cc_start: 0.7052 (m-40) cc_final: 0.6741 (m-40) REVERT: B 269 GLU cc_start: 0.6294 (tt0) cc_final: 0.5939 (tt0) REVERT: B 330 MET cc_start: 0.6239 (mpp) cc_final: 0.5881 (mpp) REVERT: B 342 THR cc_start: 0.8480 (t) cc_final: 0.8209 (p) REVERT: B 484 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7441 (mmmm) REVERT: B 511 ILE cc_start: 0.8174 (tt) cc_final: 0.7822 (tp) REVERT: B 536 GLU cc_start: 0.6654 (tp30) cc_final: 0.6449 (tp30) REVERT: B 659 MET cc_start: 0.6999 (mtp) cc_final: 0.6430 (mtp) REVERT: B 719 ARG cc_start: 0.6891 (mmm-85) cc_final: 0.6479 (tpt-90) REVERT: B 734 GLN cc_start: 0.7003 (mp10) cc_final: 0.6363 (mp10) REVERT: B 740 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7791 (mtmm) REVERT: B 744 LYS cc_start: 0.7877 (tttt) cc_final: 0.7567 (tttm) REVERT: B 800 GLU cc_start: 0.7691 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 819 ARG cc_start: 0.7980 (tpt170) cc_final: 0.7695 (tpt170) REVERT: B 822 MET cc_start: 0.6870 (tpp) cc_final: 0.6545 (tpp) REVERT: B 860 LYS cc_start: 0.8839 (tppt) cc_final: 0.8121 (tppt) REVERT: B 861 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 873 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 922 MET cc_start: 0.6781 (mmm) cc_final: 0.6496 (mmm) REVERT: C 64 THR cc_start: 0.7423 (t) cc_final: 0.7097 (p) REVERT: C 96 MET cc_start: 0.7617 (ttp) cc_final: 0.7164 (tmm) REVERT: C 125 PHE cc_start: 0.7676 (m-80) cc_final: 0.6998 (m-80) REVERT: C 132 PHE cc_start: 0.7628 (m-80) cc_final: 0.7138 (m-10) REVERT: E 95 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8100 (mt-10) REVERT: E 96 MET cc_start: 0.8076 (ttm) cc_final: 0.7577 (ttm) REVERT: E 124 ASP cc_start: 0.6973 (t0) cc_final: 0.6634 (t0) REVERT: E 125 PHE cc_start: 0.7043 (m-10) cc_final: 0.6599 (m-10) REVERT: E 185 MET cc_start: 0.7028 (tpp) cc_final: 0.6820 (mpp) REVERT: D 20 MET cc_start: 0.2834 (pmm) cc_final: 0.2105 (ppp) REVERT: D 138 MET cc_start: 0.7797 (tpp) cc_final: 0.7319 (mmm) outliers start: 38 outliers final: 22 residues processed: 397 average time/residue: 0.3281 time to fit residues: 195.6916 Evaluate side-chains 384 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 225 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 234 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 120 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 223 optimal weight: 0.0770 chunk 180 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.210740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.177762 restraints weight = 39481.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183200 restraints weight = 22066.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.186965 restraints weight = 14034.362| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19652 Z= 0.138 Angle : 0.667 16.629 26445 Z= 0.342 Chirality : 0.043 0.225 2856 Planarity : 0.004 0.069 3436 Dihedral : 7.004 102.386 2599 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.88 % Allowed : 14.31 % Favored : 83.81 % 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 (0.17), residues: 2363 helix: 0.49 (0.14), residues: 1356 sheet: -0.37 (0.40), residues: 159 loop : -0.57 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 816 HIS 0.005 0.001 HIS A 492 PHE 0.035 0.002 PHE E 55 TYR 0.023 0.002 TYR A 103 ARG 0.005 0.000 ARG B 870 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 1089) hydrogen bonds : angle 5.35141 ( 3162) covalent geometry : bond 0.00295 (19651) covalent geometry : angle 0.66709 (26445) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 364 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.4976 (mmm) cc_final: 0.4595 (mmm) REVERT: A 77 MET cc_start: 0.6952 (mpp) cc_final: 0.6458 (mpp) REVERT: A 89 ASP cc_start: 0.6260 (t0) cc_final: 0.6002 (t0) REVERT: A 90 MET cc_start: 0.4775 (tmm) cc_final: 0.4566 (tmm) REVERT: A 98 GLU cc_start: 0.7518 (tp30) cc_final: 0.7226 (tm-30) REVERT: A 145 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7525 (mmtp) REVERT: A 224 ASN cc_start: 0.5089 (t0) cc_final: 0.4847 (t0) REVERT: A 240 ASN cc_start: 0.7698 (t0) cc_final: 0.7390 (t0) REVERT: A 241 SER cc_start: 0.8469 (t) cc_final: 0.8015 (p) REVERT: A 352 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6887 (mp) REVERT: A 397 LYS cc_start: 0.7994 (mttt) cc_final: 0.7705 (mptt) REVERT: A 499 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6833 (tp30) REVERT: A 500 GLU cc_start: 0.6575 (tt0) cc_final: 0.6111 (mt-10) REVERT: A 551 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7873 (mmmt) REVERT: A 562 ASN cc_start: 0.6197 (m110) cc_final: 0.5804 (m110) REVERT: A 685 ASP cc_start: 0.7342 (m-30) cc_final: 0.6960 (m-30) REVERT: A 690 MET cc_start: 0.5259 (ttt) cc_final: 0.4354 (ttt) REVERT: A 724 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6921 (tt) REVERT: A 799 MET cc_start: 0.7398 (mmt) cc_final: 0.6615 (mmt) REVERT: A 822 MET cc_start: 0.6389 (ppp) cc_final: 0.5880 (ppp) REVERT: A 845 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6836 (tpp-160) REVERT: A 847 LYS cc_start: 0.7170 (mtmm) cc_final: 0.6881 (pttm) REVERT: A 852 MET cc_start: 0.8127 (tmm) cc_final: 0.7607 (tmm) REVERT: A 870 ARG cc_start: 0.7691 (ptm160) cc_final: 0.6964 (ptm-80) REVERT: B 45 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 129 LYS cc_start: 0.8083 (tttt) cc_final: 0.7625 (ttpt) REVERT: B 133 VAL cc_start: 0.7898 (p) cc_final: 0.7346 (t) REVERT: B 179 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6811 (mt-10) REVERT: B 232 ASN cc_start: 0.6920 (m-40) cc_final: 0.6645 (m-40) REVERT: B 266 TYR cc_start: 0.7000 (m-80) cc_final: 0.6140 (m-80) REVERT: B 269 GLU cc_start: 0.6340 (tt0) cc_final: 0.6122 (tt0) REVERT: B 293 LYS cc_start: 0.8115 (pttm) cc_final: 0.7813 (ptmt) REVERT: B 330 MET cc_start: 0.6166 (mpp) cc_final: 0.5078 (mpp) REVERT: B 342 THR cc_start: 0.8405 (t) cc_final: 0.8040 (p) REVERT: B 467 ILE cc_start: 0.8432 (mp) cc_final: 0.8054 (mp) REVERT: B 536 GLU cc_start: 0.6665 (tp30) cc_final: 0.6131 (tp30) REVERT: B 719 ARG cc_start: 0.6927 (mmm-85) cc_final: 0.6620 (tpt-90) REVERT: B 734 GLN cc_start: 0.7006 (mp10) cc_final: 0.6500 (mp10) REVERT: B 740 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7729 (mtmm) REVERT: B 744 LYS cc_start: 0.7801 (tttt) cc_final: 0.7525 (tttm) REVERT: B 800 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 819 ARG cc_start: 0.7972 (tpt170) cc_final: 0.7251 (mmm160) REVERT: B 822 MET cc_start: 0.6893 (tpp) cc_final: 0.6460 (tpt) REVERT: B 847 LYS cc_start: 0.8576 (tptt) cc_final: 0.7888 (mttt) REVERT: B 859 LEU cc_start: 0.8712 (mp) cc_final: 0.7975 (tt) REVERT: B 860 LYS cc_start: 0.8846 (tppt) cc_final: 0.8113 (tppt) REVERT: B 861 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 873 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7948 (mp) REVERT: B 922 MET cc_start: 0.6804 (mmm) cc_final: 0.6497 (mmm) REVERT: C 64 THR cc_start: 0.7295 (t) cc_final: 0.6986 (p) REVERT: C 96 MET cc_start: 0.7676 (ttp) cc_final: 0.7195 (tmm) REVERT: C 125 PHE cc_start: 0.7694 (m-80) cc_final: 0.7050 (m-80) REVERT: C 132 PHE cc_start: 0.7633 (m-80) cc_final: 0.7145 (m-10) REVERT: E 95 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8177 (tt0) REVERT: E 96 MET cc_start: 0.8076 (ttm) cc_final: 0.7540 (ttm) REVERT: E 125 PHE cc_start: 0.7002 (m-10) cc_final: 0.6628 (m-10) REVERT: D 20 MET cc_start: 0.2910 (pmm) cc_final: 0.2369 (ppp) REVERT: D 138 MET cc_start: 0.7835 (tpp) cc_final: 0.7484 (mmm) REVERT: F 137 ASN cc_start: 0.8709 (m-40) cc_final: 0.8408 (t0) outliers start: 39 outliers final: 24 residues processed: 376 average time/residue: 0.3363 time to fit residues: 189.7829 Evaluate side-chains 376 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 349 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.208856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.175323 restraints weight = 39111.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180606 restraints weight = 21985.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.184399 restraints weight = 14128.184| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19652 Z= 0.157 Angle : 0.663 10.810 26445 Z= 0.339 Chirality : 0.043 0.233 2856 Planarity : 0.004 0.058 3436 Dihedral : 6.884 99.803 2599 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.46 % Allowed : 15.71 % Favored : 81.83 % 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: 0.07 (0.17), residues: 2363 helix: 0.60 (0.14), residues: 1348 sheet: -0.50 (0.40), residues: 156 loop : -0.60 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.034 0.002 PHE E 55 TYR 0.020 0.002 TYR A 287 ARG 0.005 0.000 ARG B 671 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 1089) hydrogen bonds : angle 5.27167 ( 3162) covalent geometry : bond 0.00338 (19651) covalent geometry : angle 0.66290 (26445) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 77 MET cc_start: 0.6907 (mpp) cc_final: 0.6522 (mpp) REVERT: A 98 GLU cc_start: 0.7476 (tp30) cc_final: 0.7271 (tm-30) REVERT: A 102 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6600 (tp) REVERT: A 224 ASN cc_start: 0.5202 (t0) cc_final: 0.4959 (t0) REVERT: A 241 SER cc_start: 0.8453 (t) cc_final: 0.7942 (p) REVERT: A 301 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5101 (mt) REVERT: A 314 SER cc_start: 0.6915 (t) cc_final: 0.6714 (m) REVERT: A 397 LYS cc_start: 0.8043 (mttt) cc_final: 0.7727 (mptt) REVERT: A 441 THR cc_start: 0.7636 (m) cc_final: 0.7375 (t) REVERT: A 499 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6886 (tp30) REVERT: A 500 GLU cc_start: 0.6670 (tt0) cc_final: 0.6375 (mt-10) REVERT: A 551 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7910 (mmmt) REVERT: A 562 ASN cc_start: 0.6178 (m110) cc_final: 0.5790 (m110) REVERT: A 685 ASP cc_start: 0.7296 (m-30) cc_final: 0.6899 (m-30) REVERT: A 690 MET cc_start: 0.5351 (ttt) cc_final: 0.4381 (ttt) REVERT: A 799 MET cc_start: 0.7479 (mmt) cc_final: 0.6704 (mmt) REVERT: A 800 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 822 MET cc_start: 0.6379 (ppp) cc_final: 0.5860 (ppp) REVERT: A 845 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6934 (tpp-160) REVERT: A 846 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: A 847 LYS cc_start: 0.7109 (mtmm) cc_final: 0.6800 (pttm) REVERT: A 852 MET cc_start: 0.8124 (tmm) cc_final: 0.7559 (tmm) REVERT: A 870 ARG cc_start: 0.7722 (ptm160) cc_final: 0.7020 (ptm-80) REVERT: B 129 LYS cc_start: 0.8091 (tttt) cc_final: 0.7636 (ttpt) REVERT: B 133 VAL cc_start: 0.7844 (p) cc_final: 0.7346 (t) REVERT: B 149 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7290 (mp0) REVERT: B 179 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6954 (mt-10) REVERT: B 232 ASN cc_start: 0.6934 (m-40) cc_final: 0.6630 (m-40) REVERT: B 266 TYR cc_start: 0.7048 (m-80) cc_final: 0.6160 (m-80) REVERT: B 269 GLU cc_start: 0.6409 (tt0) cc_final: 0.6169 (tt0) REVERT: B 293 LYS cc_start: 0.8138 (pttm) cc_final: 0.7836 (ptmt) REVERT: B 342 THR cc_start: 0.8348 (t) cc_final: 0.8133 (p) REVERT: B 450 LYS cc_start: 0.7835 (mttt) cc_final: 0.7571 (mttt) REVERT: B 467 ILE cc_start: 0.8459 (mp) cc_final: 0.8086 (mp) REVERT: B 484 LYS cc_start: 0.7961 (mmmm) cc_final: 0.7676 (mmmm) REVERT: B 671 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: B 676 ASN cc_start: 0.7470 (t0) cc_final: 0.7221 (t0) REVERT: B 734 GLN cc_start: 0.7071 (mp10) cc_final: 0.6541 (mp10) REVERT: B 740 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7718 (mtmm) REVERT: B 744 LYS cc_start: 0.7841 (tttt) cc_final: 0.7579 (tttm) REVERT: B 773 LEU cc_start: 0.6958 (mm) cc_final: 0.6570 (mt) REVERT: B 776 MET cc_start: 0.8038 (mtt) cc_final: 0.7798 (mtt) REVERT: B 800 GLU cc_start: 0.7755 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 819 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7220 (mmm160) REVERT: B 847 LYS cc_start: 0.8576 (tptt) cc_final: 0.7871 (mttt) REVERT: B 859 LEU cc_start: 0.8720 (mp) cc_final: 0.7976 (tt) REVERT: B 860 LYS cc_start: 0.8831 (tppt) cc_final: 0.8075 (tppt) REVERT: B 861 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 873 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7841 (mp) REVERT: C 64 THR cc_start: 0.7095 (t) cc_final: 0.6826 (p) REVERT: C 78 ASN cc_start: 0.4783 (OUTLIER) cc_final: 0.3752 (p0) REVERT: C 96 MET cc_start: 0.7745 (ttp) cc_final: 0.7205 (tmm) REVERT: C 125 PHE cc_start: 0.7705 (m-80) cc_final: 0.7037 (m-80) REVERT: C 132 PHE cc_start: 0.7622 (m-80) cc_final: 0.7152 (m-10) REVERT: C 156 MET cc_start: 0.5644 (mmt) cc_final: 0.5142 (mmt) REVERT: E 95 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8167 (tt0) REVERT: E 96 MET cc_start: 0.8045 (ttm) cc_final: 0.7546 (ttm) REVERT: E 125 PHE cc_start: 0.7133 (m-10) cc_final: 0.6870 (m-10) REVERT: D 20 MET cc_start: 0.3174 (pmm) cc_final: 0.2652 (ppp) REVERT: D 100 THR cc_start: 0.8378 (p) cc_final: 0.8068 (t) REVERT: D 127 CYS cc_start: 0.7192 (m) cc_final: 0.6906 (p) REVERT: D 138 MET cc_start: 0.7837 (tpp) cc_final: 0.7486 (mmm) outliers start: 51 outliers final: 24 residues processed: 395 average time/residue: 0.3256 time to fit residues: 194.5871 Evaluate side-chains 387 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 0.1980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 HIS B 564 GLN B 890 GLN F 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.209160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.176127 restraints weight = 38687.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.181306 restraints weight = 22067.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.184890 restraints weight = 14212.952| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19652 Z= 0.144 Angle : 0.659 10.026 26445 Z= 0.336 Chirality : 0.043 0.353 2856 Planarity : 0.004 0.059 3436 Dihedral : 6.708 98.400 2599 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.22 % Allowed : 16.63 % Favored : 81.16 % 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 (0.17), residues: 2363 helix: 0.64 (0.14), residues: 1342 sheet: -0.50 (0.39), residues: 156 loop : -0.55 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.039 0.002 PHE E 55 TYR 0.025 0.002 TYR B 142 ARG 0.006 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 1089) hydrogen bonds : angle 5.21267 ( 3162) covalent geometry : bond 0.00307 (19651) covalent geometry : angle 0.65910 (26445) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6856 (mpp) cc_final: 0.6530 (mpp) REVERT: A 102 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6293 (tp) REVERT: A 241 SER cc_start: 0.8430 (t) cc_final: 0.7843 (p) REVERT: A 352 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 397 LYS cc_start: 0.8018 (mttt) cc_final: 0.7729 (mptt) REVERT: A 499 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6861 (tp30) REVERT: A 500 GLU cc_start: 0.6676 (tt0) cc_final: 0.6216 (mt-10) REVERT: A 515 MET cc_start: 0.6720 (ppp) cc_final: 0.6516 (ppp) REVERT: A 551 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7888 (mmmt) REVERT: A 562 ASN cc_start: 0.6163 (m110) cc_final: 0.5803 (m110) REVERT: A 685 ASP cc_start: 0.7296 (m-30) cc_final: 0.6793 (m-30) REVERT: A 690 MET cc_start: 0.5335 (ttt) cc_final: 0.4440 (ttt) REVERT: A 789 GLN cc_start: 0.7769 (mt0) cc_final: 0.7401 (mt0) REVERT: A 799 MET cc_start: 0.7437 (mmt) cc_final: 0.6702 (mmt) REVERT: A 822 MET cc_start: 0.6365 (ppp) cc_final: 0.5815 (ppp) REVERT: A 845 ARG cc_start: 0.7192 (tpp-160) cc_final: 0.6785 (tpp-160) REVERT: A 846 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 847 LYS cc_start: 0.7035 (mtmm) cc_final: 0.6699 (pttm) REVERT: A 852 MET cc_start: 0.8120 (tmm) cc_final: 0.7555 (tmm) REVERT: A 872 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 45 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 129 LYS cc_start: 0.8046 (tttt) cc_final: 0.7626 (ttpt) REVERT: B 133 VAL cc_start: 0.7832 (p) cc_final: 0.7288 (t) REVERT: B 179 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6918 (mt-10) REVERT: B 232 ASN cc_start: 0.6837 (m-40) cc_final: 0.6565 (m-40) REVERT: B 266 TYR cc_start: 0.7032 (m-80) cc_final: 0.6111 (m-80) REVERT: B 293 LYS cc_start: 0.8148 (pttm) cc_final: 0.7848 (ptmt) REVERT: B 467 ILE cc_start: 0.8448 (mp) cc_final: 0.8068 (mp) REVERT: B 484 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7641 (mmmm) REVERT: B 548 PHE cc_start: 0.8059 (t80) cc_final: 0.7736 (t80) REVERT: B 659 MET cc_start: 0.6993 (mmm) cc_final: 0.6739 (mmm) REVERT: B 671 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7715 (mmm-85) REVERT: B 676 ASN cc_start: 0.7477 (t0) cc_final: 0.7249 (t0) REVERT: B 719 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6732 (tpt90) REVERT: B 734 GLN cc_start: 0.7052 (mp10) cc_final: 0.6536 (mp10) REVERT: B 740 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7719 (mtmm) REVERT: B 744 LYS cc_start: 0.7827 (tttt) cc_final: 0.7511 (tttm) REVERT: B 773 LEU cc_start: 0.6905 (mm) cc_final: 0.6700 (mp) REVERT: B 800 GLU cc_start: 0.7760 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 819 ARG cc_start: 0.7840 (tpt170) cc_final: 0.7137 (mmm160) REVERT: B 847 LYS cc_start: 0.8544 (tptt) cc_final: 0.7849 (mttt) REVERT: B 859 LEU cc_start: 0.8693 (mp) cc_final: 0.7964 (tt) REVERT: B 860 LYS cc_start: 0.8813 (tppt) cc_final: 0.8054 (tppt) REVERT: B 861 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 873 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7944 (mp) REVERT: C 64 THR cc_start: 0.6945 (t) cc_final: 0.6714 (p) REVERT: C 78 ASN cc_start: 0.4808 (OUTLIER) cc_final: 0.4532 (p0) REVERT: C 96 MET cc_start: 0.7724 (ttp) cc_final: 0.7194 (tmm) REVERT: C 125 PHE cc_start: 0.7658 (m-80) cc_final: 0.7011 (m-80) REVERT: C 132 PHE cc_start: 0.7616 (m-80) cc_final: 0.7098 (m-10) REVERT: C 144 GLU cc_start: 0.7053 (tp30) cc_final: 0.6679 (tp30) REVERT: C 156 MET cc_start: 0.5394 (mmt) cc_final: 0.4947 (mmt) REVERT: E 95 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8144 (mt-10) REVERT: E 96 MET cc_start: 0.7990 (ttm) cc_final: 0.7527 (ttm) REVERT: E 125 PHE cc_start: 0.7119 (m-10) cc_final: 0.6811 (m-10) REVERT: D 20 MET cc_start: 0.3257 (pmm) cc_final: 0.2779 (ppp) REVERT: D 138 MET cc_start: 0.7787 (tpp) cc_final: 0.7492 (mmm) outliers start: 46 outliers final: 25 residues processed: 390 average time/residue: 0.3204 time to fit residues: 188.5361 Evaluate side-chains 371 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 134 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 221 optimal weight: 0.0030 chunk 2 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 188 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** 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 = 0.4696 r_free = 0.4696 target = 0.209086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.176314 restraints weight = 38539.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.181287 restraints weight = 22218.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.184642 restraints weight = 14492.236| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19652 Z= 0.144 Angle : 0.674 13.809 26445 Z= 0.342 Chirality : 0.044 0.315 2856 Planarity : 0.004 0.061 3436 Dihedral : 6.615 97.131 2599 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 17.64 % Favored : 80.24 % 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 (0.17), residues: 2363 helix: 0.61 (0.14), residues: 1344 sheet: -0.40 (0.40), residues: 157 loop : -0.59 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.036 0.002 PHE E 55 TYR 0.019 0.002 TYR A 103 ARG 0.004 0.000 ARG B 870 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 1089) hydrogen bonds : angle 5.15537 ( 3162) covalent geometry : bond 0.00306 (19651) covalent geometry : angle 0.67373 (26445) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 344 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 241 SER cc_start: 0.8435 (t) cc_final: 0.7913 (p) REVERT: A 397 LYS cc_start: 0.8022 (mttt) cc_final: 0.7730 (mptt) REVERT: A 499 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6869 (tp30) REVERT: A 500 GLU cc_start: 0.6685 (tt0) cc_final: 0.6387 (mt-10) REVERT: A 515 MET cc_start: 0.6920 (ppp) cc_final: 0.6624 (ppp) REVERT: A 528 MET cc_start: 0.7586 (mmt) cc_final: 0.7334 (mmm) REVERT: A 551 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7888 (mmmt) REVERT: A 562 ASN cc_start: 0.6197 (m110) cc_final: 0.5822 (m110) REVERT: A 685 ASP cc_start: 0.7352 (m-30) cc_final: 0.6821 (m-30) REVERT: A 690 MET cc_start: 0.5355 (ttt) cc_final: 0.5001 (ttt) REVERT: A 799 MET cc_start: 0.7451 (mmt) cc_final: 0.6662 (mmt) REVERT: A 816 TRP cc_start: 0.7070 (m-90) cc_final: 0.6816 (m-90) REVERT: A 822 MET cc_start: 0.6375 (ppp) cc_final: 0.5784 (ppp) REVERT: A 845 ARG cc_start: 0.7286 (tpp-160) cc_final: 0.6895 (tpp-160) REVERT: A 846 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 847 LYS cc_start: 0.7080 (mtmm) cc_final: 0.6752 (pttm) REVERT: A 852 MET cc_start: 0.8152 (tmm) cc_final: 0.7623 (tmm) REVERT: B 45 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 129 LYS cc_start: 0.8027 (tttt) cc_final: 0.7585 (ttpt) REVERT: B 133 VAL cc_start: 0.7809 (p) cc_final: 0.7257 (t) REVERT: B 179 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 232 ASN cc_start: 0.6847 (m-40) cc_final: 0.6544 (m-40) REVERT: B 266 TYR cc_start: 0.7029 (m-80) cc_final: 0.6113 (m-80) REVERT: B 293 LYS cc_start: 0.8151 (pttm) cc_final: 0.7859 (ptmt) REVERT: B 467 ILE cc_start: 0.8435 (mp) cc_final: 0.8071 (mp) REVERT: B 548 PHE cc_start: 0.8101 (t80) cc_final: 0.7790 (t80) REVERT: B 671 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7699 (mmm-85) REVERT: B 719 ARG cc_start: 0.6995 (mmm160) cc_final: 0.6730 (tpt-90) REVERT: B 734 GLN cc_start: 0.7039 (mp10) cc_final: 0.6365 (mp10) REVERT: B 740 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7731 (mtmm) REVERT: B 744 LYS cc_start: 0.7835 (tttt) cc_final: 0.7573 (tttm) REVERT: B 773 LEU cc_start: 0.6928 (mm) cc_final: 0.6564 (mt) REVERT: B 847 LYS cc_start: 0.8533 (tptt) cc_final: 0.7852 (mmtt) REVERT: B 859 LEU cc_start: 0.8733 (mp) cc_final: 0.7991 (tt) REVERT: B 860 LYS cc_start: 0.8819 (tppt) cc_final: 0.8057 (tppt) REVERT: B 861 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 873 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 64 THR cc_start: 0.6902 (t) cc_final: 0.6686 (p) REVERT: C 78 ASN cc_start: 0.4771 (OUTLIER) cc_final: 0.4428 (p0) REVERT: C 96 MET cc_start: 0.7719 (ttp) cc_final: 0.7190 (tmm) REVERT: C 125 PHE cc_start: 0.7697 (m-80) cc_final: 0.6990 (m-80) REVERT: C 132 PHE cc_start: 0.7564 (m-80) cc_final: 0.7092 (m-10) REVERT: C 144 GLU cc_start: 0.7055 (tp30) cc_final: 0.6817 (tp30) REVERT: C 156 MET cc_start: 0.5585 (mmt) cc_final: 0.5066 (mmm) REVERT: E 94 GLU cc_start: 0.8154 (pm20) cc_final: 0.7754 (pm20) REVERT: E 96 MET cc_start: 0.7967 (ttm) cc_final: 0.7539 (ttm) REVERT: E 156 MET cc_start: 0.3732 (mmm) cc_final: 0.3471 (mmp) REVERT: E 169 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6776 (mm-30) REVERT: D 20 MET cc_start: 0.3278 (pmm) cc_final: 0.2865 (ppp) REVERT: D 138 MET cc_start: 0.7818 (tpp) cc_final: 0.7547 (mmm) REVERT: F 83 LEU cc_start: 0.2262 (mt) cc_final: 0.2026 (mt) outliers start: 44 outliers final: 30 residues processed: 366 average time/residue: 0.3327 time to fit residues: 183.8935 Evaluate side-chains 370 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 337 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** 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 = 0.4683 r_free = 0.4683 target = 0.207757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.174085 restraints weight = 38818.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.179393 restraints weight = 21885.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183051 restraints weight = 14102.873| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19652 Z= 0.183 Angle : 0.700 11.173 26445 Z= 0.359 Chirality : 0.044 0.291 2856 Planarity : 0.004 0.060 3436 Dihedral : 6.651 92.791 2599 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 17.88 % Favored : 79.81 % 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: -0.07 (0.17), residues: 2363 helix: 0.52 (0.14), residues: 1342 sheet: -0.56 (0.39), residues: 163 loop : -0.69 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 816 HIS 0.024 0.002 HIS B 358 PHE 0.036 0.002 PHE E 55 TYR 0.023 0.002 TYR A 162 ARG 0.004 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1089) hydrogen bonds : angle 5.23408 ( 3162) covalent geometry : bond 0.00393 (19651) covalent geometry : angle 0.69972 (26445) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.3075 (OUTLIER) cc_final: 0.2761 (ttm) REVERT: A 179 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5808 (tt0) REVERT: A 330 MET cc_start: 0.5957 (mmm) cc_final: 0.5665 (mmt) REVERT: A 397 LYS cc_start: 0.8066 (mttt) cc_final: 0.7714 (mptt) REVERT: A 499 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6925 (tp30) REVERT: A 500 GLU cc_start: 0.6746 (tt0) cc_final: 0.6245 (mt-10) REVERT: A 515 MET cc_start: 0.7017 (ppp) cc_final: 0.6650 (ppp) REVERT: A 551 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7928 (mmmt) REVERT: A 562 ASN cc_start: 0.6418 (m110) cc_final: 0.6053 (m110) REVERT: A 685 ASP cc_start: 0.7344 (m-30) cc_final: 0.6807 (m-30) REVERT: A 719 ARG cc_start: 0.7108 (ttp80) cc_final: 0.6780 (mtp85) REVERT: A 799 MET cc_start: 0.7536 (mmt) cc_final: 0.6777 (mmt) REVERT: A 816 TRP cc_start: 0.6948 (OUTLIER) cc_final: 0.6660 (m-90) REVERT: A 822 MET cc_start: 0.6382 (ppp) cc_final: 0.5748 (ppp) REVERT: A 845 ARG cc_start: 0.7258 (tpp-160) cc_final: 0.6901 (tpp-160) REVERT: A 846 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 847 LYS cc_start: 0.7090 (mtmm) cc_final: 0.6706 (pttm) REVERT: A 852 MET cc_start: 0.8180 (tmm) cc_final: 0.7735 (tmm) REVERT: B 129 LYS cc_start: 0.8063 (tttt) cc_final: 0.7616 (ttpt) REVERT: B 133 VAL cc_start: 0.8005 (p) cc_final: 0.7492 (t) REVERT: B 169 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6941 (ttm110) REVERT: B 179 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6899 (mt-10) REVERT: B 222 GLN cc_start: 0.7347 (mm110) cc_final: 0.7108 (mm110) REVERT: B 232 ASN cc_start: 0.6924 (m-40) cc_final: 0.6466 (m-40) REVERT: B 234 LYS cc_start: 0.7036 (tmmt) cc_final: 0.6446 (tmmt) REVERT: B 266 TYR cc_start: 0.7155 (m-80) cc_final: 0.6217 (m-80) REVERT: B 448 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6338 (tm-30) REVERT: B 548 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80) REVERT: B 671 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: B 676 ASN cc_start: 0.7580 (t0) cc_final: 0.6811 (p0) REVERT: B 734 GLN cc_start: 0.7118 (mp10) cc_final: 0.6516 (mp10) REVERT: B 740 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7727 (mtmm) REVERT: B 776 MET cc_start: 0.8158 (mtt) cc_final: 0.7892 (mtt) REVERT: B 847 LYS cc_start: 0.8544 (tptt) cc_final: 0.7881 (mmtt) REVERT: B 859 LEU cc_start: 0.8708 (mp) cc_final: 0.7969 (tt) REVERT: B 860 LYS cc_start: 0.8805 (tppt) cc_final: 0.8060 (tppt) REVERT: B 861 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 873 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 897 ASN cc_start: 0.7193 (m110) cc_final: 0.6987 (m110) REVERT: C 70 ASP cc_start: 0.8541 (m-30) cc_final: 0.8130 (m-30) REVERT: C 78 ASN cc_start: 0.4842 (OUTLIER) cc_final: 0.4518 (p0) REVERT: C 132 PHE cc_start: 0.7630 (m-80) cc_final: 0.7141 (m-10) REVERT: C 144 GLU cc_start: 0.7092 (tp30) cc_final: 0.6802 (tp30) REVERT: C 156 MET cc_start: 0.5702 (mmt) cc_final: 0.5206 (mmm) REVERT: E 94 GLU cc_start: 0.8194 (pm20) cc_final: 0.7830 (pm20) REVERT: E 96 MET cc_start: 0.8033 (ttm) cc_final: 0.7413 (ttm) REVERT: E 169 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6851 (mm-30) REVERT: D 20 MET cc_start: 0.3405 (pmm) cc_final: 0.2765 (ppp) REVERT: D 138 MET cc_start: 0.7842 (tpp) cc_final: 0.7621 (mmm) REVERT: F 33 PHE cc_start: 0.4165 (t80) cc_final: 0.3894 (t80) REVERT: F 69 MET cc_start: 0.5266 (mmp) cc_final: 0.4985 (mmp) REVERT: F 83 LEU cc_start: 0.2353 (mt) cc_final: 0.2111 (mt) outliers start: 48 outliers final: 31 residues processed: 386 average time/residue: 0.3227 time to fit residues: 188.9624 Evaluate side-chains 385 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 816 TRP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** 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 = 0.4691 r_free = 0.4691 target = 0.208719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.175786 restraints weight = 38083.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.180911 restraints weight = 21695.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184462 restraints weight = 13966.901| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19652 Z= 0.150 Angle : 0.705 11.350 26445 Z= 0.358 Chirality : 0.044 0.281 2856 Planarity : 0.004 0.066 3436 Dihedral : 6.569 93.002 2599 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.12 % Allowed : 18.75 % Favored : 79.13 % 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: -0.07 (0.17), residues: 2363 helix: 0.53 (0.14), residues: 1349 sheet: -0.53 (0.39), residues: 170 loop : -0.73 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.040 0.002 PHE E 55 TYR 0.028 0.002 TYR A 386 ARG 0.008 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 1089) hydrogen bonds : angle 5.15844 ( 3162) covalent geometry : bond 0.00323 (19651) covalent geometry : angle 0.70460 (26445) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.6135 (mt-10) cc_final: 0.5775 (tt0) REVERT: A 241 SER cc_start: 0.8405 (t) cc_final: 0.7907 (p) REVERT: A 301 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.5026 (mt) REVERT: A 330 MET cc_start: 0.5932 (mmm) cc_final: 0.5675 (mmt) REVERT: A 397 LYS cc_start: 0.8053 (mttt) cc_final: 0.7723 (mptt) REVERT: A 493 MET cc_start: 0.7283 (mmt) cc_final: 0.6612 (mmt) REVERT: A 499 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6874 (tp30) REVERT: A 500 GLU cc_start: 0.6679 (tt0) cc_final: 0.6004 (mt-10) REVERT: A 515 MET cc_start: 0.7005 (ppp) cc_final: 0.6594 (ppp) REVERT: A 551 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7908 (mmmt) REVERT: A 562 ASN cc_start: 0.6333 (m110) cc_final: 0.5983 (m110) REVERT: A 685 ASP cc_start: 0.7304 (m-30) cc_final: 0.6797 (m-30) REVERT: A 719 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6751 (mtp85) REVERT: A 772 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6414 (tt) REVERT: A 799 MET cc_start: 0.7470 (mmt) cc_final: 0.6723 (mmt) REVERT: A 816 TRP cc_start: 0.6928 (OUTLIER) cc_final: 0.6687 (m-90) REVERT: A 822 MET cc_start: 0.6351 (ppp) cc_final: 0.5724 (ppp) REVERT: A 845 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6902 (tpp-160) REVERT: A 846 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 847 LYS cc_start: 0.6973 (mtmm) cc_final: 0.6613 (pttm) REVERT: A 852 MET cc_start: 0.8160 (tmm) cc_final: 0.7783 (tmm) REVERT: B 113 MET cc_start: 0.4880 (pmm) cc_final: 0.4095 (pmm) REVERT: B 129 LYS cc_start: 0.8046 (tttt) cc_final: 0.7586 (ttpt) REVERT: B 133 VAL cc_start: 0.7987 (p) cc_final: 0.7505 (t) REVERT: B 169 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6908 (ttm110) REVERT: B 179 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6888 (mt-10) REVERT: B 222 GLN cc_start: 0.7284 (mm110) cc_final: 0.7044 (mm110) REVERT: B 232 ASN cc_start: 0.6679 (m-40) cc_final: 0.6338 (m-40) REVERT: B 234 LYS cc_start: 0.6930 (tmmt) cc_final: 0.6408 (tmmt) REVERT: B 243 ARG cc_start: 0.6148 (mmp80) cc_final: 0.5748 (mmp80) REVERT: B 266 TYR cc_start: 0.7067 (m-80) cc_final: 0.6176 (m-80) REVERT: B 293 LYS cc_start: 0.8129 (pttm) cc_final: 0.7834 (ptmt) REVERT: B 467 ILE cc_start: 0.8530 (mp) cc_final: 0.8138 (mp) REVERT: B 548 PHE cc_start: 0.8042 (t80) cc_final: 0.7756 (t80) REVERT: B 671 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7735 (mmm-85) REVERT: B 676 ASN cc_start: 0.7561 (t0) cc_final: 0.6824 (p0) REVERT: B 719 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6794 (tpt-90) REVERT: B 734 GLN cc_start: 0.7126 (mp10) cc_final: 0.6443 (mp10) REVERT: B 740 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7726 (mtmm) REVERT: B 811 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7419 (tt) REVERT: B 847 LYS cc_start: 0.8516 (tptt) cc_final: 0.7799 (mmtt) REVERT: B 859 LEU cc_start: 0.8688 (mp) cc_final: 0.7962 (tt) REVERT: B 860 LYS cc_start: 0.8777 (tppt) cc_final: 0.8028 (tppt) REVERT: B 861 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 873 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 897 ASN cc_start: 0.7149 (m110) cc_final: 0.6931 (m110) REVERT: C 78 ASN cc_start: 0.4810 (OUTLIER) cc_final: 0.4519 (p0) REVERT: C 95 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: C 132 PHE cc_start: 0.7641 (m-80) cc_final: 0.7122 (m-10) REVERT: C 144 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tp30) REVERT: E 94 GLU cc_start: 0.8118 (pm20) cc_final: 0.7728 (pm20) REVERT: E 96 MET cc_start: 0.7779 (ttm) cc_final: 0.7291 (ttm) REVERT: E 169 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6807 (mm-30) REVERT: D 20 MET cc_start: 0.3462 (pmm) cc_final: 0.2823 (ppp) REVERT: D 100 THR cc_start: 0.8173 (p) cc_final: 0.7914 (t) REVERT: F 33 PHE cc_start: 0.3993 (t80) cc_final: 0.3762 (t80) REVERT: F 69 MET cc_start: 0.5242 (mmp) cc_final: 0.5021 (mmp) REVERT: F 83 LEU cc_start: 0.2205 (mt) cc_final: 0.1930 (mt) outliers start: 44 outliers final: 28 residues processed: 382 average time/residue: 0.3421 time to fit residues: 199.5672 Evaluate side-chains 384 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 816 TRP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 213 optimal weight: 0.1980 chunk 195 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** 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 = 0.4702 r_free = 0.4702 target = 0.209305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.175414 restraints weight = 38747.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.180767 restraints weight = 21708.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184580 restraints weight = 13913.173| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19652 Z= 0.153 Angle : 0.727 15.167 26445 Z= 0.366 Chirality : 0.044 0.265 2856 Planarity : 0.004 0.064 3436 Dihedral : 6.536 92.507 2599 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 19.18 % Favored : 78.99 % 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 (0.17), residues: 2363 helix: 0.51 (0.14), residues: 1347 sheet: -0.49 (0.40), residues: 168 loop : -0.72 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.042 0.002 PHE E 55 TYR 0.026 0.002 TYR A 386 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1089) hydrogen bonds : angle 5.16037 ( 3162) covalent geometry : bond 0.00331 (19651) covalent geometry : angle 0.72743 (26445) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 354 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5790 (tt0) REVERT: A 301 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.5025 (mt) REVERT: A 330 MET cc_start: 0.5937 (mmm) cc_final: 0.5695 (mmt) REVERT: A 397 LYS cc_start: 0.8060 (mttt) cc_final: 0.7661 (mmtm) REVERT: A 499 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6889 (tp30) REVERT: A 500 GLU cc_start: 0.6655 (tt0) cc_final: 0.5999 (mt-10) REVERT: A 515 MET cc_start: 0.6997 (ppp) cc_final: 0.6557 (ppp) REVERT: A 551 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7924 (mmmt) REVERT: A 562 ASN cc_start: 0.6427 (m110) cc_final: 0.6063 (m110) REVERT: A 685 ASP cc_start: 0.7307 (m-30) cc_final: 0.6823 (m-30) REVERT: A 719 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6727 (mtp85) REVERT: A 772 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6361 (tt) REVERT: A 799 MET cc_start: 0.7448 (mmt) cc_final: 0.6693 (mmt) REVERT: A 816 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.6385 (m-90) REVERT: A 822 MET cc_start: 0.6333 (ppp) cc_final: 0.5711 (ppp) REVERT: A 845 ARG cc_start: 0.7234 (tpp-160) cc_final: 0.6934 (tpp-160) REVERT: A 846 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: A 847 LYS cc_start: 0.7025 (mtmm) cc_final: 0.6658 (pttm) REVERT: A 852 MET cc_start: 0.8187 (tmm) cc_final: 0.7730 (tmm) REVERT: B 45 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 113 MET cc_start: 0.4969 (pmm) cc_final: 0.4180 (pmm) REVERT: B 129 LYS cc_start: 0.8043 (tttt) cc_final: 0.7677 (tttm) REVERT: B 133 VAL cc_start: 0.8008 (p) cc_final: 0.7471 (t) REVERT: B 179 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6821 (mt-10) REVERT: B 222 GLN cc_start: 0.7324 (mm110) cc_final: 0.7101 (mm110) REVERT: B 232 ASN cc_start: 0.6517 (m-40) cc_final: 0.6206 (m110) REVERT: B 234 LYS cc_start: 0.6961 (tmmt) cc_final: 0.6431 (tmmt) REVERT: B 266 TYR cc_start: 0.7104 (m-80) cc_final: 0.6260 (m-80) REVERT: B 359 PHE cc_start: 0.7696 (m-80) cc_final: 0.6876 (m-80) REVERT: B 450 LYS cc_start: 0.8042 (mttt) cc_final: 0.7622 (mmtt) REVERT: B 467 ILE cc_start: 0.8480 (mp) cc_final: 0.8115 (mp) REVERT: B 548 PHE cc_start: 0.8058 (t80) cc_final: 0.7778 (t80) REVERT: B 671 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7728 (mmm-85) REVERT: B 676 ASN cc_start: 0.7538 (t0) cc_final: 0.6859 (p0) REVERT: B 719 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6775 (tpt-90) REVERT: B 734 GLN cc_start: 0.7146 (mp10) cc_final: 0.6547 (mp-120) REVERT: B 740 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7745 (mtmm) REVERT: B 811 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7426 (tt) REVERT: B 834 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.4427 (p90) REVERT: B 847 LYS cc_start: 0.8513 (tptt) cc_final: 0.7789 (mmtt) REVERT: B 859 LEU cc_start: 0.8692 (mp) cc_final: 0.7952 (tt) REVERT: B 860 LYS cc_start: 0.8769 (tppt) cc_final: 0.8027 (tppt) REVERT: B 861 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7326 (tm-30) REVERT: B 873 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 78 ASN cc_start: 0.4893 (OUTLIER) cc_final: 0.4584 (p0) REVERT: C 95 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: C 132 PHE cc_start: 0.7606 (m-80) cc_final: 0.7112 (m-10) REVERT: C 144 GLU cc_start: 0.7074 (tp30) cc_final: 0.6804 (tp30) REVERT: C 156 MET cc_start: 0.5589 (mmm) cc_final: 0.5142 (mmm) REVERT: E 94 GLU cc_start: 0.8125 (pm20) cc_final: 0.7726 (pm20) REVERT: E 169 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6873 (mm-30) REVERT: D 20 MET cc_start: 0.3466 (pmm) cc_final: 0.2883 (ppp) REVERT: D 100 THR cc_start: 0.8130 (p) cc_final: 0.7871 (t) REVERT: F 33 PHE cc_start: 0.3949 (t80) cc_final: 0.3717 (t80) REVERT: F 69 MET cc_start: 0.5339 (mmp) cc_final: 0.5129 (mmp) REVERT: F 83 LEU cc_start: 0.2335 (mt) cc_final: 0.2055 (mt) outliers start: 38 outliers final: 28 residues processed: 373 average time/residue: 0.5095 time to fit residues: 294.1068 Evaluate side-chains 384 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 347 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 816 TRP Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 801 TYR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 109 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 231 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 220 optimal weight: 0.0060 chunk 190 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.209193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.176167 restraints weight = 38309.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.181437 restraints weight = 21903.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.184983 restraints weight = 14070.698| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19652 Z= 0.146 Angle : 0.724 14.210 26445 Z= 0.366 Chirality : 0.044 0.265 2856 Planarity : 0.005 0.192 3436 Dihedral : 6.520 95.709 2599 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.17 % Allowed : 18.84 % Favored : 78.99 % 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: -0.06 (0.17), residues: 2363 helix: 0.49 (0.14), residues: 1350 sheet: -0.39 (0.40), residues: 166 loop : -0.68 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 PHE 0.042 0.002 PHE E 55 TYR 0.025 0.002 TYR A 386 ARG 0.023 0.001 ARG A 870 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 1089) hydrogen bonds : angle 5.12502 ( 3162) covalent geometry : bond 0.00316 (19651) covalent geometry : angle 0.72406 (26445) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8437.11 seconds wall clock time: 151 minutes 13.31 seconds (9073.31 seconds total)