Starting phenix.real_space_refine on Thu Sep 18 18:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gz1_51719/09_2025/9gz1_51719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gz1_51719/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gz1_51719/09_2025/9gz1_51719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gz1_51719/09_2025/9gz1_51719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gz1_51719/09_2025/9gz1_51719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gz1_51719/09_2025/9gz1_51719.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.07, per 1000 atoms: 0.21 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: 1.67 Conformation dependent library (CDL) restraints added in 764.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.72 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: 3.14 Time building geometry restraints manager: 2.12 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 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- 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 : 14.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (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 ARG 0.043 0.004 ARG B 845 TYR 0.108 0.007 TYR A 164 PHE 0.052 0.003 PHE B 821 TRP 0.057 0.004 TRP B 829 HIS 0.012 0.002 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00535 (19651) covalent geometry : angle 1.12376 (26445) hydrogen bonds : bond 0.14076 ( 1089) hydrogen bonds : angle 7.16579 ( 3162) 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 : 0.721 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: 0.7506 (t) REVERT: A 240 ASN cc_start: 0.7571 (t0) cc_final: 0.7300 (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: 0.6242 (mt-10) REVERT: A 608 LEU cc_start: 0.8024 (tp) cc_final: 0.7754 (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: 0.7453 (mp0) 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: 0.7015 (m-40) REVERT: B 264 GLU cc_start: 0.6941 (tt0) cc_final: 0.6632 (tt0) REVERT: B 266 TYR cc_start: 0.6820 (m-80) cc_final: 0.6465 (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: 0.6739 (tm-30) REVERT: B 457 ILE cc_start: 0.6907 (mt) cc_final: 0.5371 (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: 0.5944 (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: 0.7436 (tm-30) REVERT: C 125 PHE cc_start: 0.7674 (m-80) cc_final: 0.7026 (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: 0.7866 (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: 0.6652 (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: 0.7999 (t0) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1489 time to fit residues: 102.0027 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 235 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 923 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.209223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.176298 restraints weight = 39185.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.181785 restraints weight = 21957.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185471 restraints weight = 13875.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.187798 restraints weight = 9808.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.189392 restraints weight = 7670.450| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19652 Z= 0.181 Angle : 0.752 9.295 26445 Z= 0.392 Chirality : 0.047 0.185 2856 Planarity : 0.005 0.101 3436 Dihedral : 7.515 101.992 2599 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.30 % Allowed : 9.01 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2363 helix: 0.09 (0.13), residues: 1355 sheet: -0.62 (0.40), residues: 157 loop : -0.64 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 870 TYR 0.028 0.002 TYR A 722 PHE 0.023 0.002 PHE D 21 TRP 0.028 0.002 TRP B 829 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00388 (19651) covalent geometry : angle 0.75154 (26445) hydrogen bonds : bond 0.05410 ( 1089) hydrogen bonds : angle 5.78707 ( 3162) Misc. bond : bond 0.00269 ( 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 427 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 400 time to evaluate : 0.725 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 25 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 98 GLU cc_start: 0.7734 (tp30) cc_final: 0.7309 (tm-30) REVERT: A 195 PHE cc_start: 0.6755 (m-80) cc_final: 0.6431 (m-80) REVERT: A 215 THR cc_start: 0.7850 (p) cc_final: 0.7594 (t) REVERT: A 224 ASN cc_start: 0.6242 (m-40) cc_final: 0.6001 (t0) REVERT: A 240 ASN cc_start: 0.7680 (t0) cc_final: 0.7341 (t0) REVERT: A 241 SER cc_start: 0.8453 (t) cc_final: 0.8145 (p) REVERT: A 257 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7701 (mmtm) REVERT: A 397 LYS cc_start: 0.7974 (mttt) cc_final: 0.7718 (mptt) REVERT: A 433 GLU cc_start: 0.6069 (tm-30) cc_final: 0.5701 (tm-30) REVERT: A 493 MET cc_start: 0.7175 (mmt) cc_final: 0.6676 (mpp) REVERT: A 499 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6686 (tp30) REVERT: A 500 GLU cc_start: 0.6621 (tt0) cc_final: 0.6167 (mt-10) REVERT: A 562 ASN cc_start: 0.5819 (m110) cc_final: 0.5541 (m110) REVERT: A 685 ASP cc_start: 0.7377 (m-30) cc_final: 0.6906 (m-30) REVERT: A 690 MET cc_start: 0.5289 (ttt) cc_final: 0.4608 (ttt) REVERT: A 709 PHE cc_start: 0.6834 (m-80) cc_final: 0.6564 (m-80) REVERT: A 799 MET cc_start: 0.7317 (mmt) cc_final: 0.6744 (mmt) REVERT: A 804 LEU cc_start: 0.8645 (mm) cc_final: 0.8329 (mm) REVERT: A 822 MET cc_start: 0.6315 (ppp) cc_final: 0.5902 (ppp) REVERT: A 845 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6945 (tpp-160) REVERT: A 852 MET cc_start: 0.8111 (tmm) cc_final: 0.7590 (tmm) REVERT: B 129 LYS cc_start: 0.8065 (tttt) cc_final: 0.7573 (ttpt) REVERT: B 149 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7226 (mp0) REVERT: B 179 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 232 ASN cc_start: 0.7132 (m-40) cc_final: 0.6882 (m-40) REVERT: B 266 TYR cc_start: 0.6624 (m-80) cc_final: 0.6414 (m-80) REVERT: B 269 GLU cc_start: 0.6271 (tt0) cc_final: 0.5912 (tt0) REVERT: B 293 LYS cc_start: 0.8294 (ptmt) cc_final: 0.8016 (pttm) REVERT: B 330 MET cc_start: 0.6401 (mpp) cc_final: 0.5968 (mpp) REVERT: B 484 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7482 (mmmm) REVERT: B 659 MET cc_start: 0.7144 (mtp) cc_final: 0.6595 (mtp) REVERT: B 734 GLN cc_start: 0.6865 (mp10) cc_final: 0.6619 (mp10) REVERT: B 740 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7747 (mtmm) REVERT: B 800 GLU cc_start: 0.7632 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 819 ARG cc_start: 0.8023 (tpt170) cc_final: 0.7271 (mmm160) REVERT: B 860 LYS cc_start: 0.8885 (tppt) cc_final: 0.8161 (tppt) REVERT: B 861 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 872 GLU cc_start: 0.7977 (mt-10) cc_final: 0.6991 (mt-10) REVERT: B 922 MET cc_start: 0.6900 (mmm) cc_final: 0.6673 (mmm) REVERT: C 64 THR cc_start: 0.7845 (t) cc_final: 0.7479 (p) REVERT: C 96 MET cc_start: 0.7550 (ttp) cc_final: 0.7132 (tmm) REVERT: C 125 PHE cc_start: 0.7577 (m-80) cc_final: 0.6955 (m-80) REVERT: E 65 LEU cc_start: 0.7261 (tp) cc_final: 0.6957 (tt) REVERT: E 95 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8133 (mt-10) REVERT: E 96 MET cc_start: 0.8097 (ttm) cc_final: 0.7512 (ttm) REVERT: E 124 ASP cc_start: 0.7056 (t0) cc_final: 0.6641 (t0) REVERT: E 125 PHE cc_start: 0.7067 (m-10) cc_final: 0.6720 (m-10) REVERT: D 20 MET cc_start: 0.2946 (pmm) cc_final: 0.2141 (ppp) REVERT: D 56 MET cc_start: 0.6978 (ttm) cc_final: 0.6753 (ttt) REVERT: D 138 MET cc_start: 0.7718 (tpp) cc_final: 0.7182 (mmm) outliers start: 27 outliers final: 13 residues processed: 408 average time/residue: 0.1478 time to fit residues: 91.1486 Evaluate side-chains 385 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 372 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 923 ASN 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 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 148 optimal weight: 7.9990 chunk 184 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 141 optimal weight: 0.0040 chunk 201 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 157 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.0470 overall best weight: 0.1928 ------------------------------------------------------------------------------- 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 498 GLN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN B 44 GLN B 104 ASN B 482 ASN B 486 GLN B 711 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.210230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177118 restraints weight = 39842.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.182623 restraints weight = 22136.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.186382 restraints weight = 14028.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.188745 restraints weight = 9942.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.190517 restraints weight = 7778.519| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19652 Z= 0.144 Angle : 0.672 10.116 26445 Z= 0.348 Chirality : 0.043 0.181 2856 Planarity : 0.004 0.088 3436 Dihedral : 7.154 99.970 2599 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 12.39 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2363 helix: 0.40 (0.13), residues: 1352 sheet: -0.55 (0.39), residues: 169 loop : -0.51 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 870 TYR 0.025 0.002 TYR A 722 PHE 0.025 0.002 PHE F 118 TRP 0.049 0.002 TRP A 816 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00304 (19651) covalent geometry : angle 0.67186 (26445) hydrogen bonds : bond 0.04738 ( 1089) hydrogen bonds : angle 5.47078 ( 3162) Misc. bond : bond 0.00074 ( 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 417 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 0.718 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 25 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 98 GLU cc_start: 0.7479 (tp30) cc_final: 0.7192 (tm-30) REVERT: A 103 TYR cc_start: 0.6845 (m-80) cc_final: 0.6637 (m-80) REVERT: A 195 PHE cc_start: 0.6698 (m-80) cc_final: 0.6108 (m-80) REVERT: A 215 THR cc_start: 0.7812 (p) cc_final: 0.7568 (t) REVERT: A 235 THR cc_start: 0.6205 (p) cc_final: 0.5687 (t) REVERT: A 240 ASN cc_start: 0.7744 (t0) cc_final: 0.7441 (t0) REVERT: A 241 SER cc_start: 0.8461 (t) cc_final: 0.8057 (p) REVERT: A 397 LYS cc_start: 0.7945 (mttt) cc_final: 0.7717 (mptt) REVERT: A 433 GLU cc_start: 0.5928 (tm-30) cc_final: 0.5726 (tt0) REVERT: A 499 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6231 (tp30) REVERT: A 500 GLU cc_start: 0.6545 (tt0) cc_final: 0.6116 (mt-10) REVERT: A 562 ASN cc_start: 0.5887 (m110) cc_final: 0.5567 (m110) REVERT: A 589 ASN cc_start: 0.6341 (t0) cc_final: 0.5910 (t0) REVERT: A 690 MET cc_start: 0.5270 (ttt) cc_final: 0.4055 (ttt) REVERT: A 799 MET cc_start: 0.7328 (mmt) cc_final: 0.6574 (mmt) REVERT: A 804 LEU cc_start: 0.8663 (mm) cc_final: 0.8321 (mm) REVERT: A 822 MET cc_start: 0.6365 (ppp) cc_final: 0.5890 (ppp) REVERT: A 845 ARG cc_start: 0.7262 (tpp-160) cc_final: 0.6896 (tpp-160) REVERT: A 852 MET cc_start: 0.8110 (tmm) cc_final: 0.7635 (tmm) REVERT: A 870 ARG cc_start: 0.7641 (ptm160) cc_final: 0.6902 (ptm-80) REVERT: B 129 LYS cc_start: 0.8018 (tttt) cc_final: 0.7534 (ttpt) REVERT: B 170 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7234 (pt0) REVERT: B 232 ASN cc_start: 0.6903 (m-40) cc_final: 0.6673 (m-40) REVERT: B 269 GLU cc_start: 0.6264 (tt0) cc_final: 0.5888 (tt0) REVERT: B 330 MET cc_start: 0.6135 (mpp) cc_final: 0.5096 (mpp) REVERT: B 342 THR cc_start: 0.8441 (t) cc_final: 0.8186 (p) REVERT: B 467 ILE cc_start: 0.8460 (mp) cc_final: 0.8096 (mp) REVERT: B 511 ILE cc_start: 0.8103 (tt) cc_final: 0.7769 (tp) REVERT: B 536 GLU cc_start: 0.6520 (tp30) cc_final: 0.6167 (tp30) REVERT: B 719 ARG cc_start: 0.6878 (mmm-85) cc_final: 0.6636 (tpt90) REVERT: B 734 GLN cc_start: 0.6919 (mp10) cc_final: 0.6520 (mp10) REVERT: B 740 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7764 (mtmm) REVERT: B 744 LYS cc_start: 0.7870 (tttt) cc_final: 0.7610 (tttm) REVERT: B 800 GLU cc_start: 0.7645 (tm-30) cc_final: 0.6893 (tm-30) REVERT: B 819 ARG cc_start: 0.7953 (tpt170) cc_final: 0.7203 (mmm160) REVERT: B 822 MET cc_start: 0.6815 (tpp) cc_final: 0.6522 (tpp) REVERT: B 860 LYS cc_start: 0.8836 (tppt) cc_final: 0.8115 (tppt) REVERT: B 861 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 873 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 922 MET cc_start: 0.6819 (mmm) cc_final: 0.6559 (mmm) REVERT: C 64 THR cc_start: 0.7381 (t) cc_final: 0.7062 (p) REVERT: C 96 MET cc_start: 0.7569 (ttp) cc_final: 0.7122 (tmm) REVERT: C 125 PHE cc_start: 0.7616 (m-80) cc_final: 0.6967 (m-80) REVERT: E 96 MET cc_start: 0.7987 (ttm) cc_final: 0.7498 (ttm) REVERT: E 124 ASP cc_start: 0.6774 (t0) cc_final: 0.6550 (t0) REVERT: E 125 PHE cc_start: 0.6952 (m-10) cc_final: 0.6559 (m-10) REVERT: D 20 MET cc_start: 0.2900 (pmm) cc_final: 0.2334 (ppp) REVERT: D 138 MET cc_start: 0.7796 (tpp) cc_final: 0.7339 (mmm) outliers start: 42 outliers final: 22 residues processed: 390 average time/residue: 0.1418 time to fit residues: 84.4569 Evaluate side-chains 378 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 355 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 659 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 482 ASN 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 106 PHE 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: 0.7980 chunk 60 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 451 GLN B 651 HIS B 890 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.208251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.174951 restraints weight = 39453.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.180249 restraints weight = 22110.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.183996 restraints weight = 14181.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.186283 restraints weight = 10061.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.188057 restraints weight = 7963.134| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19652 Z= 0.186 Angle : 0.696 16.292 26445 Z= 0.357 Chirality : 0.044 0.231 2856 Planarity : 0.004 0.069 3436 Dihedral : 7.034 103.755 2599 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.88 % Allowed : 14.80 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2363 helix: 0.48 (0.14), residues: 1345 sheet: -0.70 (0.38), residues: 169 loop : -0.60 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 671 TYR 0.023 0.002 TYR A 722 PHE 0.027 0.002 PHE A 359 TRP 0.064 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00400 (19651) covalent geometry : angle 0.69563 (26445) hydrogen bonds : bond 0.04763 ( 1089) hydrogen bonds : angle 5.40045 ( 3162) Misc. bond : bond 0.00036 ( 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 415 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 0.696 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: A 77 MET cc_start: 0.7005 (mpp) cc_final: 0.6516 (mpp) REVERT: A 98 GLU cc_start: 0.7622 (tp30) cc_final: 0.7365 (tm-30) REVERT: A 195 PHE cc_start: 0.6684 (m-80) cc_final: 0.6109 (m-80) REVERT: A 215 THR cc_start: 0.7913 (p) cc_final: 0.7679 (t) REVERT: A 224 ASN cc_start: 0.5140 (t0) cc_final: 0.4855 (t0) REVERT: A 241 SER cc_start: 0.8396 (t) cc_final: 0.7875 (p) REVERT: A 301 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.4412 (tp) REVERT: A 397 LYS cc_start: 0.7975 (mttt) cc_final: 0.7695 (mptt) REVERT: A 433 GLU cc_start: 0.5989 (tm-30) cc_final: 0.5665 (tm-30) REVERT: A 493 MET cc_start: 0.7260 (mmt) cc_final: 0.6760 (mpp) REVERT: A 499 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6886 (tp30) REVERT: A 500 GLU cc_start: 0.6698 (tt0) cc_final: 0.6394 (mt-10) REVERT: A 551 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7883 (mmmt) REVERT: A 562 ASN cc_start: 0.6163 (m110) cc_final: 0.5778 (m110) REVERT: A 685 ASP cc_start: 0.7431 (m-30) cc_final: 0.7004 (m-30) REVERT: A 690 MET cc_start: 0.5341 (ttt) cc_final: 0.4417 (ttt) REVERT: A 709 PHE cc_start: 0.6800 (m-80) cc_final: 0.6555 (m-80) REVERT: A 799 MET cc_start: 0.7490 (mmt) cc_final: 0.6680 (mmt) REVERT: A 822 MET cc_start: 0.6393 (ppp) cc_final: 0.5873 (ppp) REVERT: A 845 ARG cc_start: 0.7274 (tpp-160) cc_final: 0.6901 (tpp-160) REVERT: A 852 MET cc_start: 0.8092 (tmm) cc_final: 0.7487 (tmm) REVERT: B 129 LYS cc_start: 0.8059 (tttt) cc_final: 0.7535 (ttpt) REVERT: B 170 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7243 (pt0) REVERT: B 179 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6394 (mm-30) REVERT: B 232 ASN cc_start: 0.7029 (m-40) cc_final: 0.6629 (m-40) REVERT: B 266 TYR cc_start: 0.7166 (m-80) cc_final: 0.6499 (m-80) REVERT: B 269 GLU cc_start: 0.6454 (tt0) cc_final: 0.6090 (tt0) REVERT: B 330 MET cc_start: 0.6188 (mpp) cc_final: 0.5848 (mpp) REVERT: B 342 THR cc_start: 0.8422 (t) cc_final: 0.8045 (p) REVERT: B 671 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7099 (mmm160) REVERT: B 719 ARG cc_start: 0.6944 (mmm-85) cc_final: 0.6642 (tpt-90) REVERT: B 734 GLN cc_start: 0.6971 (mp10) cc_final: 0.6333 (mp10) REVERT: B 740 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7743 (mtmm) REVERT: B 744 LYS cc_start: 0.7859 (tttt) cc_final: 0.7593 (tttm) REVERT: B 800 GLU cc_start: 0.7714 (tm-30) cc_final: 0.6943 (tm-30) REVERT: B 819 ARG cc_start: 0.7972 (tpt170) cc_final: 0.7259 (mmm160) REVERT: B 822 MET cc_start: 0.6870 (tpp) cc_final: 0.6508 (tpt) REVERT: B 859 LEU cc_start: 0.8724 (mp) cc_final: 0.8014 (tt) REVERT: B 860 LYS cc_start: 0.8845 (tppt) cc_final: 0.8121 (tppt) REVERT: B 861 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7264 (tm-30) REVERT: B 873 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 922 MET cc_start: 0.6747 (mmm) cc_final: 0.6407 (mmm) REVERT: C 64 THR cc_start: 0.7314 (t) cc_final: 0.7005 (p) REVERT: C 96 MET cc_start: 0.7654 (ttp) cc_final: 0.7182 (tmm) REVERT: C 125 PHE cc_start: 0.7684 (m-80) cc_final: 0.7041 (m-80) REVERT: C 132 PHE cc_start: 0.7642 (m-80) cc_final: 0.7238 (m-10) REVERT: C 156 MET cc_start: 0.5622 (mmt) cc_final: 0.4777 (mmt) REVERT: E 96 MET cc_start: 0.8024 (ttm) cc_final: 0.7501 (ttm) REVERT: E 125 PHE cc_start: 0.7127 (m-10) cc_final: 0.6759 (m-10) REVERT: E 185 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6772 (mpp) REVERT: D 20 MET cc_start: 0.3059 (pmm) cc_final: 0.2463 (ppp) REVERT: D 138 MET cc_start: 0.7824 (tpp) cc_final: 0.7583 (mmm) REVERT: F 137 ASN cc_start: 0.8705 (m-40) cc_final: 0.8408 (t0) outliers start: 39 outliers final: 27 residues processed: 389 average time/residue: 0.1445 time to fit residues: 85.5233 Evaluate side-chains 387 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 VAL 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 539 MET Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 847 LYS 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 455 TYR 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 106 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 185 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** 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 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN B 44 GLN B 451 GLN B 482 ASN B 564 GLN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.207887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.174935 restraints weight = 38980.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.180023 restraints weight = 22433.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.183582 restraints weight = 14532.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.185670 restraints weight = 10399.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.187324 restraints weight = 8248.238| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19652 Z= 0.169 Angle : 0.670 10.837 26445 Z= 0.345 Chirality : 0.043 0.213 2856 Planarity : 0.004 0.058 3436 Dihedral : 6.915 103.658 2599 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.99 % Allowed : 15.47 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.17), residues: 2363 helix: 0.54 (0.14), residues: 1347 sheet: -0.54 (0.40), residues: 159 loop : -0.68 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 671 TYR 0.022 0.002 TYR A 103 PHE 0.025 0.002 PHE F 118 TRP 0.077 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00361 (19651) covalent geometry : angle 0.67011 (26445) hydrogen bonds : bond 0.04539 ( 1089) hydrogen bonds : angle 5.32580 ( 3162) Misc. bond : bond 0.00026 ( 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 429 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 367 time to evaluate : 0.710 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: A 25 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8124 (mt-10) REVERT: A 77 MET cc_start: 0.6932 (mpp) cc_final: 0.6360 (mpp) REVERT: A 102 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6289 (tp) REVERT: A 215 THR cc_start: 0.7962 (p) cc_final: 0.7756 (t) REVERT: A 241 SER cc_start: 0.8374 (t) cc_final: 0.7762 (p) REVERT: A 301 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.4054 (tp) REVERT: A 352 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6801 (mp) REVERT: A 397 LYS cc_start: 0.7971 (mttt) cc_final: 0.7709 (mptt) REVERT: A 433 GLU cc_start: 0.6080 (tm-30) cc_final: 0.5857 (tt0) REVERT: A 441 THR cc_start: 0.7642 (m) cc_final: 0.7387 (t) REVERT: A 493 MET cc_start: 0.7242 (mmt) cc_final: 0.6751 (mpp) REVERT: A 500 GLU cc_start: 0.6730 (tt0) cc_final: 0.6438 (mt-10) REVERT: A 528 MET cc_start: 0.7543 (mmt) cc_final: 0.7265 (mmm) REVERT: A 551 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7883 (mmmt) REVERT: A 562 ASN cc_start: 0.6234 (m110) cc_final: 0.5877 (m110) REVERT: A 685 ASP cc_start: 0.7346 (m-30) cc_final: 0.6941 (m-30) REVERT: A 690 MET cc_start: 0.5360 (ttt) cc_final: 0.4577 (ttt) REVERT: A 799 MET cc_start: 0.7456 (mmt) cc_final: 0.6685 (mmt) REVERT: A 800 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 822 MET cc_start: 0.6363 (ppp) cc_final: 0.5844 (ppp) REVERT: A 845 ARG cc_start: 0.7276 (tpp-160) cc_final: 0.6859 (tpp-160) REVERT: A 852 MET cc_start: 0.8103 (tmm) cc_final: 0.7560 (tmm) REVERT: B 129 LYS cc_start: 0.8044 (tttt) cc_final: 0.7585 (ttpt) REVERT: B 133 VAL cc_start: 0.7713 (t) cc_final: 0.7423 (t) REVERT: B 149 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7271 (mp0) REVERT: B 170 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7212 (pt0) REVERT: B 179 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6422 (mm-30) REVERT: B 232 ASN cc_start: 0.6967 (m-40) cc_final: 0.6546 (m110) REVERT: B 234 LYS cc_start: 0.7016 (tmmt) cc_final: 0.6592 (tmmt) REVERT: B 266 TYR cc_start: 0.7141 (m-80) cc_final: 0.6346 (m-80) REVERT: B 269 GLU cc_start: 0.6430 (tt0) cc_final: 0.6147 (tt0) REVERT: B 293 LYS cc_start: 0.8131 (pttm) cc_final: 0.7830 (ptmt) REVERT: B 330 MET cc_start: 0.6171 (mpp) cc_final: 0.5736 (mpp) REVERT: B 484 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7674 (mmmm) REVERT: B 503 LYS cc_start: 0.8072 (tttp) cc_final: 0.7835 (tmtt) REVERT: B 504 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6129 (mm-30) REVERT: B 671 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7335 (mmm-85) REVERT: B 734 GLN cc_start: 0.7006 (mp10) cc_final: 0.6484 (mp10) REVERT: B 740 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7727 (mtmm) REVERT: B 744 LYS cc_start: 0.7852 (tttt) cc_final: 0.7625 (tttm) REVERT: B 773 LEU cc_start: 0.7074 (mm) cc_final: 0.6648 (mt) REVERT: B 800 GLU cc_start: 0.7730 (tm-30) cc_final: 0.6975 (tm-30) REVERT: B 819 ARG cc_start: 0.7894 (tpt170) cc_final: 0.7218 (mmm160) REVERT: B 847 LYS cc_start: 0.8569 (tptt) cc_final: 0.7844 (mmtt) REVERT: B 859 LEU cc_start: 0.8735 (mp) cc_final: 0.8002 (tt) REVERT: B 860 LYS cc_start: 0.8837 (tppt) cc_final: 0.8075 (tppt) REVERT: B 861 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 873 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7942 (mp) REVERT: C 64 THR cc_start: 0.7089 (t) cc_final: 0.6817 (p) REVERT: C 78 ASN cc_start: 0.4929 (OUTLIER) cc_final: 0.3871 (p0) REVERT: C 96 MET cc_start: 0.7741 (ttp) cc_final: 0.7211 (tmm) REVERT: C 125 PHE cc_start: 0.7630 (m-80) cc_final: 0.6974 (m-80) REVERT: C 132 PHE cc_start: 0.7578 (m-80) cc_final: 0.7088 (m-10) REVERT: E 96 MET cc_start: 0.8000 (ttm) cc_final: 0.7518 (ttm) REVERT: E 125 PHE cc_start: 0.7121 (m-10) cc_final: 0.6877 (m-10) REVERT: D 20 MET cc_start: 0.3141 (pmm) cc_final: 0.2581 (ppp) REVERT: D 127 CYS cc_start: 0.7243 (m) cc_final: 0.6953 (p) REVERT: D 138 MET cc_start: 0.7824 (tpp) cc_final: 0.7499 (mmm) outliers start: 62 outliers final: 32 residues processed: 398 average time/residue: 0.1409 time to fit residues: 86.5506 Evaluate side-chains 388 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 351 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 352 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 847 LYS 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 455 TYR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 782 SER 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 E residue 152 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 159 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 196 optimal weight: 0.0970 chunk 7 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.209259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.176314 restraints weight = 38591.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.181366 restraints weight = 22194.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184890 restraints weight = 14448.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.187370 restraints weight = 10324.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.188455 restraints weight = 8058.665| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.3511 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= 0.144 Angle : 0.667 10.515 26445 Z= 0.338 Chirality : 0.043 0.357 2856 Planarity : 0.004 0.059 3436 Dihedral : 6.806 100.518 2599 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.51 % Allowed : 17.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2363 helix: 0.59 (0.14), residues: 1342 sheet: -0.42 (0.42), residues: 152 loop : -0.64 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 870 TYR 0.023 0.002 TYR B 142 PHE 0.026 0.002 PHE B 244 TRP 0.066 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00310 (19651) covalent geometry : angle 0.66724 (26445) hydrogen bonds : bond 0.04368 ( 1089) hydrogen bonds : angle 5.26759 ( 3162) Misc. bond : bond 0.00035 ( 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 408 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 356 time to evaluate : 0.731 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: 0.8376 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 77 MET cc_start: 0.6897 (mpp) cc_final: 0.6493 (mpp) REVERT: A 98 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 215 THR cc_start: 0.7910 (p) cc_final: 0.7706 (t) REVERT: A 241 SER cc_start: 0.8369 (t) cc_final: 0.7812 (p) REVERT: A 301 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.4652 (mt) REVERT: A 397 LYS cc_start: 0.7994 (mttt) cc_final: 0.7728 (mptt) REVERT: A 433 GLU cc_start: 0.6046 (tm-30) cc_final: 0.5824 (tt0) REVERT: A 499 GLU cc_start: 0.7218 (tp30) cc_final: 0.7011 (tp30) REVERT: A 500 GLU cc_start: 0.6723 (tt0) cc_final: 0.6410 (mt-10) REVERT: A 528 MET cc_start: 0.7513 (mmt) cc_final: 0.7293 (mmp) REVERT: A 551 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7880 (mmmt) REVERT: A 562 ASN cc_start: 0.6094 (m110) cc_final: 0.5757 (m110) REVERT: A 685 ASP cc_start: 0.7374 (m-30) cc_final: 0.6995 (m-30) REVERT: A 709 PHE cc_start: 0.6903 (m-80) cc_final: 0.6686 (m-80) REVERT: A 789 GLN cc_start: 0.7759 (mt0) cc_final: 0.7426 (mt0) REVERT: A 799 MET cc_start: 0.7430 (mmt) cc_final: 0.6657 (mmt) REVERT: A 800 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 822 MET cc_start: 0.6343 (ppp) cc_final: 0.5797 (ppp) REVERT: A 845 ARG cc_start: 0.7271 (tpp-160) cc_final: 0.6664 (tpm170) REVERT: A 852 MET cc_start: 0.8090 (tmm) cc_final: 0.7510 (tmm) REVERT: B 129 LYS cc_start: 0.8005 (tttt) cc_final: 0.7559 (ttpt) REVERT: B 133 VAL cc_start: 0.7679 (t) cc_final: 0.7328 (t) REVERT: B 170 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7172 (pt0) REVERT: B 179 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6422 (mm-30) REVERT: B 232 ASN cc_start: 0.6874 (m-40) cc_final: 0.6561 (m110) REVERT: B 266 TYR cc_start: 0.7103 (m-80) cc_final: 0.6364 (m-80) REVERT: B 269 GLU cc_start: 0.6486 (tt0) cc_final: 0.6100 (tt0) REVERT: B 293 LYS cc_start: 0.8143 (pttm) cc_final: 0.7853 (ptmt) REVERT: B 467 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 503 LYS cc_start: 0.8137 (tttp) cc_final: 0.7919 (tmtt) REVERT: B 504 GLU cc_start: 0.6432 (mm-30) cc_final: 0.6169 (mm-30) REVERT: B 671 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7222 (mmm-85) REVERT: B 713 ILE cc_start: 0.1428 (OUTLIER) cc_final: 0.0399 (mm) REVERT: B 734 GLN cc_start: 0.7036 (mp10) cc_final: 0.6381 (mp10) REVERT: B 740 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7701 (mtmm) REVERT: B 744 LYS cc_start: 0.7866 (tttt) cc_final: 0.7631 (tttm) REVERT: B 773 LEU cc_start: 0.7001 (mm) cc_final: 0.6775 (mp) REVERT: B 800 GLU cc_start: 0.7756 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 819 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7155 (mmm160) REVERT: B 847 LYS cc_start: 0.8559 (tptt) cc_final: 0.7836 (mmtt) REVERT: B 859 LEU cc_start: 0.8695 (mp) cc_final: 0.7965 (tt) REVERT: B 860 LYS cc_start: 0.8810 (tppt) cc_final: 0.8044 (tppt) REVERT: B 861 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7282 (tm-30) REVERT: B 873 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 64 THR cc_start: 0.6929 (t) cc_final: 0.6695 (p) REVERT: C 78 ASN cc_start: 0.4944 (OUTLIER) cc_final: 0.3981 (p0) REVERT: C 96 MET cc_start: 0.7672 (ttp) cc_final: 0.7163 (tmm) REVERT: C 125 PHE cc_start: 0.7637 (m-80) cc_final: 0.6990 (m-80) REVERT: C 132 PHE cc_start: 0.7624 (m-80) cc_final: 0.7076 (m-10) REVERT: C 156 MET cc_start: 0.4658 (ptm) cc_final: 0.3734 (ptm) REVERT: E 96 MET cc_start: 0.7891 (ttm) cc_final: 0.7440 (ttm) REVERT: E 125 PHE cc_start: 0.7082 (m-10) cc_final: 0.6814 (m-10) REVERT: D 20 MET cc_start: 0.3243 (pmm) cc_final: 0.2732 (ppp) REVERT: D 138 MET cc_start: 0.7791 (tpp) cc_final: 0.7477 (mmm) REVERT: F 33 PHE cc_start: 0.4184 (t80) cc_final: 0.3933 (t80) REVERT: F 83 LEU cc_start: 0.2211 (mt) cc_final: 0.1964 (mt) outliers start: 52 outliers final: 32 residues processed: 380 average time/residue: 0.1504 time to fit residues: 87.8968 Evaluate side-chains 376 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 339 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 840 LEU Chi-restraints excluded: chain A residue 847 LYS 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 319 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 455 TYR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 713 ILE 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 78 ASN 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 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 46 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.207949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.174265 restraints weight = 38989.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.179302 restraints weight = 22005.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183127 restraints weight = 14488.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.185407 restraints weight = 10303.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.187347 restraints weight = 8102.171| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19652 Z= 0.171 Angle : 0.688 13.634 26445 Z= 0.350 Chirality : 0.044 0.296 2856 Planarity : 0.004 0.061 3436 Dihedral : 6.748 97.976 2599 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.60 % Allowed : 17.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2363 helix: 0.53 (0.14), residues: 1345 sheet: -0.56 (0.39), residues: 164 loop : -0.72 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 243 TYR 0.020 0.002 TYR A 722 PHE 0.029 0.002 PHE B 244 TRP 0.087 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00370 (19651) covalent geometry : angle 0.68819 (26445) hydrogen bonds : bond 0.04475 ( 1089) hydrogen bonds : angle 5.26657 ( 3162) Misc. bond : bond 0.00029 ( 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 413 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 0.650 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 77 MET cc_start: 0.6970 (mpp) cc_final: 0.6569 (mpp) REVERT: A 98 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 179 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5440 (tt0) REVERT: A 215 THR cc_start: 0.7923 (p) cc_final: 0.7721 (t) REVERT: A 241 SER cc_start: 0.8330 (t) cc_final: 0.7786 (p) REVERT: A 301 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.4230 (tp) REVERT: A 397 LYS cc_start: 0.8008 (mttt) cc_final: 0.7711 (mptt) REVERT: A 433 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5809 (tt0) REVERT: A 500 GLU cc_start: 0.6682 (tt0) cc_final: 0.6320 (mt-10) REVERT: A 528 MET cc_start: 0.7641 (mmt) cc_final: 0.7440 (mmt) REVERT: A 551 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7913 (mmmt) REVERT: A 562 ASN cc_start: 0.6215 (m110) cc_final: 0.5877 (m110) REVERT: A 685 ASP cc_start: 0.7390 (m-30) cc_final: 0.6814 (m-30) REVERT: A 719 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6712 (mtp85) REVERT: A 799 MET cc_start: 0.7479 (mmt) cc_final: 0.6757 (mmt) REVERT: A 800 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 816 TRP cc_start: 0.7080 (m-90) cc_final: 0.6805 (m-90) REVERT: A 822 MET cc_start: 0.6364 (ppp) cc_final: 0.5786 (ppp) REVERT: A 845 ARG cc_start: 0.7370 (tpp-160) cc_final: 0.6717 (tpp-160) REVERT: A 852 MET cc_start: 0.8127 (tmm) cc_final: 0.7683 (tmm) REVERT: A 872 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 129 LYS cc_start: 0.8041 (tttt) cc_final: 0.7566 (ttpt) REVERT: B 133 VAL cc_start: 0.7897 (t) cc_final: 0.7541 (t) REVERT: B 170 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7171 (pt0) REVERT: B 179 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6413 (mm-30) REVERT: B 232 ASN cc_start: 0.6929 (m-40) cc_final: 0.6589 (m110) REVERT: B 234 LYS cc_start: 0.6949 (tmmt) cc_final: 0.6565 (tmmt) REVERT: B 266 TYR cc_start: 0.7126 (m-80) cc_final: 0.6331 (m-80) REVERT: B 269 GLU cc_start: 0.6553 (tt0) cc_final: 0.6184 (tt0) REVERT: B 293 LYS cc_start: 0.8160 (pttm) cc_final: 0.7850 (ptmt) REVERT: B 467 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 548 PHE cc_start: 0.8014 (t80) cc_final: 0.7717 (t80) REVERT: B 713 ILE cc_start: 0.1503 (OUTLIER) cc_final: 0.0466 (mm) REVERT: B 734 GLN cc_start: 0.7040 (mp10) cc_final: 0.6396 (mp10) REVERT: B 740 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7718 (mtmm) REVERT: B 744 LYS cc_start: 0.7897 (tttt) cc_final: 0.7682 (tttm) REVERT: B 819 ARG cc_start: 0.7854 (tpt170) cc_final: 0.7164 (mmm160) REVERT: B 847 LYS cc_start: 0.8567 (tptt) cc_final: 0.7872 (mmtm) REVERT: B 859 LEU cc_start: 0.8689 (mp) cc_final: 0.7947 (tt) REVERT: B 860 LYS cc_start: 0.8811 (tppt) cc_final: 0.8061 (tppt) REVERT: B 861 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 873 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (mp) REVERT: C 64 THR cc_start: 0.6908 (t) cc_final: 0.6700 (p) REVERT: C 70 ASP cc_start: 0.8592 (m-30) cc_final: 0.8201 (m-30) REVERT: C 78 ASN cc_start: 0.4936 (OUTLIER) cc_final: 0.4733 (p0) REVERT: C 96 MET cc_start: 0.7707 (ttp) cc_final: 0.7180 (tmm) REVERT: C 125 PHE cc_start: 0.7638 (m-80) cc_final: 0.7040 (m-80) REVERT: C 132 PHE cc_start: 0.7559 (m-80) cc_final: 0.7073 (m-10) REVERT: E 94 GLU cc_start: 0.8150 (pm20) cc_final: 0.7825 (pm20) REVERT: E 125 PHE cc_start: 0.7290 (m-10) cc_final: 0.7032 (m-10) REVERT: E 169 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6797 (mm-30) REVERT: D 20 MET cc_start: 0.3364 (pmm) cc_final: 0.2893 (ppp) REVERT: D 138 MET cc_start: 0.7803 (tpp) cc_final: 0.7530 (mmm) REVERT: F 33 PHE cc_start: 0.4139 (t80) cc_final: 0.3875 (t80) REVERT: F 83 LEU cc_start: 0.2333 (mt) cc_final: 0.2073 (mt) outliers start: 54 outliers final: 36 residues processed: 382 average time/residue: 0.1533 time to fit residues: 88.2860 Evaluate side-chains 388 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 788 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 847 LYS 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 319 THR 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 467 ILE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 713 ILE 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 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 149 LEU Chi-restraints excluded: chain E residue 65 LEU 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 F residue 150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 79 optimal weight: 0.5980 chunk 139 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 276 GLN A 372 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 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 = 0.4705 r_free = 0.4705 target = 0.210026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.177303 restraints weight = 38286.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.182401 restraints weight = 21953.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.186023 restraints weight = 14241.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.188089 restraints weight = 10160.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.189550 restraints weight = 7997.563| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.3943 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= 0.135 Angle : 0.696 14.812 26445 Z= 0.352 Chirality : 0.044 0.288 2856 Planarity : 0.005 0.173 3436 Dihedral : 6.614 99.958 2599 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.12 % Allowed : 18.51 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.17), residues: 2363 helix: 0.55 (0.14), residues: 1348 sheet: -0.46 (0.39), residues: 166 loop : -0.65 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 870 TYR 0.027 0.001 TYR A 386 PHE 0.034 0.002 PHE B 244 TRP 0.072 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00287 (19651) covalent geometry : angle 0.69590 (26445) hydrogen bonds : bond 0.04290 ( 1089) hydrogen bonds : angle 5.14848 ( 3162) Misc. bond : bond 0.00005 ( 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 412 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 368 time to evaluate : 0.445 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 98 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 169 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6646 (mtp180) REVERT: A 179 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5395 (tt0) REVERT: A 241 SER cc_start: 0.8382 (t) cc_final: 0.7926 (p) REVERT: A 301 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.4993 (mp) REVERT: A 397 LYS cc_start: 0.8041 (mttt) cc_final: 0.7728 (mptt) REVERT: A 433 GLU cc_start: 0.6063 (tm-30) cc_final: 0.5791 (tt0) REVERT: A 441 THR cc_start: 0.7542 (m) cc_final: 0.7305 (t) REVERT: A 493 MET cc_start: 0.7231 (mmt) cc_final: 0.6723 (mmt) REVERT: A 499 GLU cc_start: 0.7364 (tp30) cc_final: 0.6992 (tp30) REVERT: A 500 GLU cc_start: 0.6643 (tt0) cc_final: 0.6081 (mt-10) REVERT: A 528 MET cc_start: 0.7600 (mmt) cc_final: 0.7341 (mmm) REVERT: A 551 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7881 (mmmt) REVERT: A 562 ASN cc_start: 0.6221 (m110) cc_final: 0.5888 (m110) REVERT: A 685 ASP cc_start: 0.7394 (m-30) cc_final: 0.6803 (m-30) REVERT: A 793 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7313 (mtp85) REVERT: A 799 MET cc_start: 0.7490 (mmt) cc_final: 0.6703 (mmt) REVERT: A 800 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 804 LEU cc_start: 0.8682 (mm) cc_final: 0.8276 (mm) REVERT: A 816 TRP cc_start: 0.6990 (m-10) cc_final: 0.6708 (m-90) REVERT: A 822 MET cc_start: 0.6333 (ppp) cc_final: 0.5722 (ppp) REVERT: A 845 ARG cc_start: 0.7424 (tpp-160) cc_final: 0.6742 (tpp-160) REVERT: A 852 MET cc_start: 0.8191 (tmm) cc_final: 0.7827 (tmm) REVERT: B 113 MET cc_start: 0.4570 (OUTLIER) cc_final: 0.4361 (pmm) REVERT: B 129 LYS cc_start: 0.8002 (tttt) cc_final: 0.7521 (ttpt) REVERT: B 133 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7284 (t) REVERT: B 149 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7123 (mp0) REVERT: B 170 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7154 (pt0) REVERT: B 175 LEU cc_start: 0.6031 (mp) cc_final: 0.5782 (tt) REVERT: B 179 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6400 (mm-30) REVERT: B 232 ASN cc_start: 0.6730 (m-40) cc_final: 0.6463 (m110) REVERT: B 266 TYR cc_start: 0.7024 (m-80) cc_final: 0.6184 (m-80) REVERT: B 269 GLU cc_start: 0.6487 (tt0) cc_final: 0.6242 (tt0) REVERT: B 293 LYS cc_start: 0.8144 (pttm) cc_final: 0.7855 (ptmt) REVERT: B 357 MET cc_start: 0.6009 (mtp) cc_final: 0.5582 (mmm) REVERT: B 467 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 482 ASN cc_start: 0.6796 (t0) cc_final: 0.6456 (t0) REVERT: B 548 PHE cc_start: 0.8092 (t80) cc_final: 0.7804 (t80) REVERT: B 659 MET cc_start: 0.7172 (mmm) cc_final: 0.6774 (mmm) REVERT: B 734 GLN cc_start: 0.7103 (mp10) cc_final: 0.6537 (mp-120) REVERT: B 740 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7666 (mtmm) REVERT: B 744 LYS cc_start: 0.7873 (tttt) cc_final: 0.7629 (tttm) REVERT: B 847 LYS cc_start: 0.8561 (tptt) cc_final: 0.7878 (mmtt) REVERT: B 859 LEU cc_start: 0.8716 (mp) cc_final: 0.7987 (tt) REVERT: B 860 LYS cc_start: 0.8816 (tppt) cc_final: 0.8031 (tppt) REVERT: B 861 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7311 (tm-30) REVERT: B 873 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7968 (mp) REVERT: C 70 ASP cc_start: 0.8576 (m-30) cc_final: 0.8344 (m-30) REVERT: C 78 ASN cc_start: 0.4743 (OUTLIER) cc_final: 0.4440 (p0) REVERT: C 96 MET cc_start: 0.7714 (ttp) cc_final: 0.7199 (tmm) REVERT: C 125 PHE cc_start: 0.7685 (m-80) cc_final: 0.6993 (m-80) REVERT: C 132 PHE cc_start: 0.7602 (m-80) cc_final: 0.7091 (m-10) REVERT: E 94 GLU cc_start: 0.8135 (pm20) cc_final: 0.7872 (pm20) REVERT: E 125 PHE cc_start: 0.7126 (m-10) cc_final: 0.6867 (m-10) REVERT: E 169 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6838 (mm-30) REVERT: D 20 MET cc_start: 0.3376 (pmm) cc_final: 0.2984 (ppp) REVERT: D 100 THR cc_start: 0.8144 (p) cc_final: 0.7906 (t) REVERT: D 138 MET cc_start: 0.7811 (tpp) cc_final: 0.7588 (mmm) REVERT: F 33 PHE cc_start: 0.3907 (t80) cc_final: 0.3642 (t80) REVERT: F 83 LEU cc_start: 0.2182 (mt) cc_final: 0.1920 (mt) outliers start: 44 outliers final: 28 residues processed: 388 average time/residue: 0.1437 time to fit residues: 84.4870 Evaluate side-chains 385 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 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 788 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 319 THR 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 467 ILE 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 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 149 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 70 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 180 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 518 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 = 0.209152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.176362 restraints weight = 38159.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.181512 restraints weight = 21868.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.185124 restraints weight = 14152.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.187172 restraints weight = 10100.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.188959 restraints weight = 7996.332| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.4082 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= 0.151 Angle : 0.705 13.077 26445 Z= 0.359 Chirality : 0.044 0.270 2856 Planarity : 0.005 0.135 3436 Dihedral : 6.557 97.398 2599 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.07 % Allowed : 19.33 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2363 helix: 0.54 (0.14), residues: 1347 sheet: -0.54 (0.39), residues: 166 loop : -0.66 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 870 TYR 0.023 0.002 TYR A 386 PHE 0.036 0.002 PHE B 244 TRP 0.067 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00327 (19651) covalent geometry : angle 0.70525 (26445) hydrogen bonds : bond 0.04356 ( 1089) hydrogen bonds : angle 5.15094 ( 3162) Misc. bond : bond 0.00027 ( 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 402 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 0.723 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 29 ARG cc_start: 0.5899 (tmm-80) cc_final: 0.5617 (tmm-80) REVERT: A 98 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 169 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6658 (mtp180) REVERT: A 179 GLU cc_start: 0.5943 (mt-10) cc_final: 0.5489 (tt0) REVERT: A 241 SER cc_start: 0.8408 (t) cc_final: 0.7919 (p) REVERT: A 301 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5158 (mp) REVERT: A 397 LYS cc_start: 0.8070 (mttt) cc_final: 0.7765 (mptt) REVERT: A 433 GLU cc_start: 0.6133 (tm-30) cc_final: 0.5898 (tt0) REVERT: A 493 MET cc_start: 0.7222 (mmt) cc_final: 0.6644 (mmt) REVERT: A 499 GLU cc_start: 0.7317 (tp30) cc_final: 0.6803 (tp30) REVERT: A 500 GLU cc_start: 0.6659 (tt0) cc_final: 0.6084 (mt-10) REVERT: A 551 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7878 (mmmt) REVERT: A 562 ASN cc_start: 0.6276 (m110) cc_final: 0.5945 (m110) REVERT: A 685 ASP cc_start: 0.7340 (m-30) cc_final: 0.6824 (m-30) REVERT: A 709 PHE cc_start: 0.6552 (m-80) cc_final: 0.6316 (m-10) REVERT: A 719 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6683 (mtp85) REVERT: A 772 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6365 (tt) REVERT: A 793 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7358 (mtp85) REVERT: A 799 MET cc_start: 0.7481 (mmt) cc_final: 0.6715 (mmt) REVERT: A 800 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 816 TRP cc_start: 0.6919 (m-10) cc_final: 0.6628 (m-90) REVERT: A 822 MET cc_start: 0.6318 (ppp) cc_final: 0.5696 (ppp) REVERT: A 845 ARG cc_start: 0.7416 (tpp-160) cc_final: 0.6823 (tpm170) REVERT: A 852 MET cc_start: 0.8113 (tmm) cc_final: 0.7700 (tmm) REVERT: B 129 LYS cc_start: 0.8028 (tttt) cc_final: 0.7557 (ttpt) REVERT: B 133 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7429 (t) REVERT: B 170 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7179 (pt0) REVERT: B 179 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6488 (mm-30) REVERT: B 232 ASN cc_start: 0.6621 (m-40) cc_final: 0.6368 (m-40) REVERT: B 234 LYS cc_start: 0.6899 (tmmt) cc_final: 0.6446 (tmmt) REVERT: B 266 TYR cc_start: 0.7078 (m-80) cc_final: 0.6327 (m-80) REVERT: B 269 GLU cc_start: 0.6530 (tt0) cc_final: 0.6250 (tt0) REVERT: B 448 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6258 (tm-30) REVERT: B 467 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 482 ASN cc_start: 0.6741 (t0) cc_final: 0.6462 (t0) REVERT: B 548 PHE cc_start: 0.7948 (t80) cc_final: 0.7690 (t80) REVERT: B 659 MET cc_start: 0.7111 (mmm) cc_final: 0.6618 (mmm) REVERT: B 676 ASN cc_start: 0.7611 (t0) cc_final: 0.6576 (p0) REVERT: B 734 GLN cc_start: 0.7144 (mp10) cc_final: 0.6580 (mp-120) REVERT: B 740 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7710 (mtmm) REVERT: B 744 LYS cc_start: 0.7872 (tttt) cc_final: 0.7652 (tttm) REVERT: B 811 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7466 (tt) REVERT: B 847 LYS cc_start: 0.8560 (tptt) cc_final: 0.7875 (mmtt) REVERT: B 859 LEU cc_start: 0.8695 (mp) cc_final: 0.7974 (tt) REVERT: B 860 LYS cc_start: 0.8794 (tppt) cc_final: 0.8017 (tppt) REVERT: B 861 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 873 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 70 ASP cc_start: 0.8567 (m-30) cc_final: 0.8339 (m-30) REVERT: C 78 ASN cc_start: 0.4739 (OUTLIER) cc_final: 0.4363 (p0) REVERT: C 96 MET cc_start: 0.7677 (ttp) cc_final: 0.7203 (tmm) REVERT: C 132 PHE cc_start: 0.7580 (m-80) cc_final: 0.7015 (m-10) REVERT: E 94 GLU cc_start: 0.8085 (pm20) cc_final: 0.7850 (pm20) REVERT: E 156 MET cc_start: 0.2931 (mmp) cc_final: 0.2199 (mmp) REVERT: E 169 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6777 (mm-30) REVERT: D 20 MET cc_start: 0.3353 (pmm) cc_final: 0.2733 (ppp) REVERT: D 100 THR cc_start: 0.8169 (p) cc_final: 0.7936 (t) REVERT: F 33 PHE cc_start: 0.3840 (t80) cc_final: 0.3620 (t80) REVERT: F 69 MET cc_start: 0.5186 (mmp) cc_final: 0.4948 (mmp) REVERT: F 83 LEU cc_start: 0.2169 (mt) cc_final: 0.1888 (mt) outliers start: 43 outliers final: 27 residues processed: 379 average time/residue: 0.1488 time to fit residues: 85.4783 Evaluate side-chains 387 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 353 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 478 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 319 THR 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 467 ILE Chi-restraints excluded: chain B residue 481 THR 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 106 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU 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 69 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 179 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.209700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.176650 restraints weight = 38445.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.181779 restraints weight = 22064.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185418 restraints weight = 14227.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.187494 restraints weight = 10213.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.189414 restraints weight = 8107.333| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19652 Z= 0.148 Angle : 0.726 13.067 26445 Z= 0.369 Chirality : 0.044 0.266 2856 Planarity : 0.004 0.100 3436 Dihedral : 6.518 96.898 2599 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.07 % Allowed : 19.71 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2363 helix: 0.55 (0.14), residues: 1348 sheet: -0.58 (0.39), residues: 166 loop : -0.65 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 870 TYR 0.022 0.002 TYR A 386 PHE 0.038 0.002 PHE B 244 TRP 0.064 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00322 (19651) covalent geometry : angle 0.72554 (26445) hydrogen bonds : bond 0.04349 ( 1089) hydrogen bonds : angle 5.15043 ( 3162) Misc. bond : bond 0.00013 ( 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 401 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 358 time to evaluate : 0.723 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: A 98 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 169 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6785 (mtp180) REVERT: A 179 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5479 (tt0) REVERT: A 241 SER cc_start: 0.8402 (t) cc_final: 0.7941 (p) REVERT: A 301 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5164 (mp) REVERT: A 397 LYS cc_start: 0.8098 (mttt) cc_final: 0.7778 (mptt) REVERT: A 433 GLU cc_start: 0.6022 (tm-30) cc_final: 0.5761 (tt0) REVERT: A 493 MET cc_start: 0.7137 (mmt) cc_final: 0.6567 (mmt) REVERT: A 499 GLU cc_start: 0.7319 (tp30) cc_final: 0.6927 (tp30) REVERT: A 500 GLU cc_start: 0.6640 (tt0) cc_final: 0.6022 (mt-10) REVERT: A 551 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7890 (mmmt) REVERT: A 562 ASN cc_start: 0.6313 (m110) cc_final: 0.5987 (m110) REVERT: A 685 ASP cc_start: 0.7304 (m-30) cc_final: 0.6822 (m-30) REVERT: A 709 PHE cc_start: 0.6530 (m-80) cc_final: 0.6238 (m-10) REVERT: A 719 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6727 (mtp85) REVERT: A 772 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6350 (tt) REVERT: A 793 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7349 (mtp85) REVERT: A 799 MET cc_start: 0.7521 (mmt) cc_final: 0.6760 (mmt) REVERT: A 800 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 816 TRP cc_start: 0.6934 (m-10) cc_final: 0.6619 (m-90) REVERT: A 822 MET cc_start: 0.6296 (ppp) cc_final: 0.5685 (ppp) REVERT: A 845 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.6981 (tpp-160) REVERT: A 852 MET cc_start: 0.8144 (tmm) cc_final: 0.7719 (tmm) REVERT: A 869 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7368 (mtt180) REVERT: A 877 MET cc_start: 0.8387 (tpp) cc_final: 0.8176 (tmm) REVERT: B 129 LYS cc_start: 0.8011 (tttt) cc_final: 0.7528 (ttpt) REVERT: B 133 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7433 (t) REVERT: B 170 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7171 (pt0) REVERT: B 175 LEU cc_start: 0.6114 (mp) cc_final: 0.5860 (tt) REVERT: B 179 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6510 (mm-30) REVERT: B 232 ASN cc_start: 0.6583 (m-40) cc_final: 0.6349 (m110) REVERT: B 234 LYS cc_start: 0.6908 (tmmt) cc_final: 0.6391 (tmmt) REVERT: B 266 TYR cc_start: 0.7026 (m-80) cc_final: 0.6256 (m-80) REVERT: B 269 GLU cc_start: 0.6558 (tt0) cc_final: 0.6232 (tt0) REVERT: B 448 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6282 (tm-30) REVERT: B 467 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 482 ASN cc_start: 0.6775 (t0) cc_final: 0.6439 (t0) REVERT: B 548 PHE cc_start: 0.7990 (t80) cc_final: 0.7723 (t80) REVERT: B 659 MET cc_start: 0.7183 (mmm) cc_final: 0.6786 (mmm) REVERT: B 676 ASN cc_start: 0.7577 (t0) cc_final: 0.6706 (p0) REVERT: B 734 GLN cc_start: 0.7138 (mp10) cc_final: 0.6559 (mp-120) REVERT: B 740 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7699 (mtmm) REVERT: B 744 LYS cc_start: 0.7875 (tttt) cc_final: 0.7652 (tttm) REVERT: B 811 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7485 (tt) REVERT: B 847 LYS cc_start: 0.8536 (tptt) cc_final: 0.7857 (mmtt) REVERT: B 859 LEU cc_start: 0.8729 (mp) cc_final: 0.7991 (tt) REVERT: B 860 LYS cc_start: 0.8806 (tppt) cc_final: 0.8053 (tppt) REVERT: B 861 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 873 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 70 ASP cc_start: 0.8569 (m-30) cc_final: 0.8349 (m-30) REVERT: C 78 ASN cc_start: 0.4711 (OUTLIER) cc_final: 0.4347 (p0) REVERT: C 109 MET cc_start: 0.7058 (tmm) cc_final: 0.6854 (ppp) REVERT: C 132 PHE cc_start: 0.7625 (m-80) cc_final: 0.7039 (m-10) REVERT: E 79 PRO cc_start: 0.7786 (Cg_endo) cc_final: 0.7575 (Cg_exo) REVERT: E 94 GLU cc_start: 0.8089 (pm20) cc_final: 0.7869 (pm20) REVERT: E 169 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6790 (mm-30) REVERT: D 20 MET cc_start: 0.3374 (pmm) cc_final: 0.2775 (ppp) REVERT: D 100 THR cc_start: 0.8225 (p) cc_final: 0.7995 (t) REVERT: F 69 MET cc_start: 0.5208 (mmp) cc_final: 0.4990 (mmp) REVERT: F 83 LEU cc_start: 0.2269 (mt) cc_final: 0.2014 (mt) outliers start: 43 outliers final: 31 residues processed: 379 average time/residue: 0.1525 time to fit residues: 87.5369 Evaluate side-chains 391 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 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 772 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 352 LEU 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 467 ILE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 713 ILE 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 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain E residue 185 MET 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 195 optimal weight: 1.9990 chunk 198 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 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** 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 = 0.209923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.177100 restraints weight = 38207.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.182270 restraints weight = 22025.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.185633 restraints weight = 14304.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187918 restraints weight = 10278.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.189640 restraints weight = 8143.735| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.4374 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= 0.147 Angle : 0.727 13.201 26445 Z= 0.370 Chirality : 0.044 0.259 2856 Planarity : 0.004 0.102 3436 Dihedral : 6.490 96.258 2599 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 19.71 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2363 helix: 0.53 (0.14), residues: 1353 sheet: -0.52 (0.39), residues: 168 loop : -0.65 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 870 TYR 0.022 0.002 TYR A 386 PHE 0.038 0.002 PHE B 244 TRP 0.062 0.002 TRP A 816 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00318 (19651) covalent geometry : angle 0.72688 (26445) hydrogen bonds : bond 0.04307 ( 1089) hydrogen bonds : angle 5.13457 ( 3162) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3606.36 seconds wall clock time: 63 minutes 11.54 seconds (3791.54 seconds total)