Starting phenix.real_space_refine on Thu Aug 6 23:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol1_16936/08_2026/8ol1_16936.map" } resolution = 3.5 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= -0.017 sd= 0.929 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 Zn 1 6.06 5 P 288 5.49 5 S 53 5.16 5 C 10678 2.51 5 N 3348 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18376 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2966 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "L" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain: "M" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "N" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13861 SG CYS K 396 47.697 46.605 82.423 1.00 91.65 S ATOM 13867 SG CYS K 397 45.699 43.595 82.100 1.00 90.83 S ATOM 13926 SG CYS K 404 49.104 43.928 80.990 1.00 64.49 S Time building chain proxies: 3.64, per 1000 atoms: 0.20 Number of scatterers: 18376 At special positions: 0 Unit cell: (126.8, 109.048, 207.952, 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) Zn 1 29.99 S 53 16.00 P 288 15.00 O 4008 8.00 N 3348 7.00 C 10678 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=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 607.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " Number of angles added : 3 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 17 sheets defined 51.2% alpha, 11.7% beta 142 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.753A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.875A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.510A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.775A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.578A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.152A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.673A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 54 through 65 removed outlier: 4.238A pdb=" N LEU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.567A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 84 removed outlier: 3.532A pdb=" N ASN D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.653A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 3.749A pdb=" N GLY D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.457A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.663A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.935A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 4.108A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.601A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.688A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.621A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.586A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 4.094A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.593A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.595A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.593A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.613A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.756A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.898A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 174 Processing helix chain 'K' and resid 175 through 198 removed outlier: 4.365A pdb=" N ILE K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER K 180 " --> pdb=" O ARG K 176 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL K 186 " --> pdb=" O ALA K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 6.517A pdb=" N ALA K 202 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 264 No H-bonds generated for 'chain 'K' and resid 262 through 264' Processing helix chain 'K' and resid 272 through 289 removed outlier: 4.308A pdb=" N ASN K 289 " --> pdb=" O ALA K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 340 through 345 Processing helix chain 'K' and resid 345 through 354 removed outlier: 3.535A pdb=" N GLN K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 425 removed outlier: 3.622A pdb=" N LEU K 417 " --> pdb=" O MET K 413 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU K 418 " --> pdb=" O LYS K 414 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS K 421 " --> pdb=" O LEU K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.553A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 456 removed outlier: 3.946A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 477 Processing helix chain 'K' and resid 497 through 514 Processing helix chain 'K' and resid 516 through 522 removed outlier: 3.780A pdb=" N PHE K 519 " --> pdb=" O PHE K 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE K 522 " --> pdb=" O PHE K 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 289 removed outlier: 4.731A pdb=" N CYS L 282 " --> pdb=" O GLN L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 313 Processing helix chain 'M' and resid 33 through 39 removed outlier: 4.194A pdb=" N SER M 39 " --> pdb=" O HIS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 47 Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.562A pdb=" N LYS M 72 " --> pdb=" O HIS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 101 removed outlier: 3.953A pdb=" N LEU M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 111 removed outlier: 4.164A pdb=" N ASN M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 36 removed outlier: 3.501A pdb=" N LYS N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.941A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.627A pdb=" N ILE D 89 " --> pdb=" O ARG C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.632A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 207 through 208 removed outlier: 8.165A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 207 through 208 removed outlier: 4.239A pdb=" N VAL K 308 " --> pdb=" O ILE K 320 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR K 309 " --> pdb=" O LYS K 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 266 through 267 removed outlier: 3.589A pdb=" N ILE K 270 " --> pdb=" O GLU K 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 107 through 112 removed outlier: 5.483A pdb=" N ARG L 139 " --> pdb=" O ASP L 108 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N LEU L 110 " --> pdb=" O ALA L 137 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N ALA L 137 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 119 removed outlier: 5.305A pdb=" N VAL L 267 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS L 154 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU L 231 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS L 235 " --> pdb=" O CYS L 239 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N CYS L 239 " --> pdb=" O LYS L 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 31 through 32 removed outlier: 9.322A pdb=" N VAL M 60 " --> pdb=" O TYR M 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS M 20 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE M 62 " --> pdb=" O LYS M 20 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE M 22 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 12 through 19 Processing sheet with id=AB8, first strand: chain 'N' and resid 67 through 68 removed outlier: 3.666A pdb=" N ARG N 68 " --> pdb=" O ALA N 71 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.20 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: 4282 1.33 - 1.46: 5149 1.46 - 1.58: 9224 1.58 - 1.70: 576 1.70 - 1.82: 83 Bond restraints: 19314 Sorted by residual: bond pdb=" C5' DA I 119 " pdb=" C4' DA I 119 " ideal model delta sigma weight residual 1.512 1.550 -0.038 7.00e-03 2.04e+04 2.97e+01 bond pdb=" C5' DA J 101 " pdb=" C4' DA J 101 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.63e+01 bond pdb=" C4 DC I 83 " pdb=" N4 DC I 83 " ideal model delta sigma weight residual 1.335 1.290 0.045 9.00e-03 1.23e+04 2.53e+01 bond pdb=" C5' DG I 120 " pdb=" C4' DG I 120 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.52e+01 bond pdb=" C5' DT I 88 " pdb=" C4' DT I 88 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.49e+01 ... (remaining 19309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 18690 1.91 - 3.82: 6775 3.82 - 5.73: 1606 5.73 - 7.64: 202 7.64 - 9.55: 29 Bond angle restraints: 27302 Sorted by residual: angle pdb=" O5' DT J 34 " pdb=" C5' DT J 34 " pdb=" C4' DT J 34 " ideal model delta sigma weight residual 109.40 118.95 -9.55 8.00e-01 1.56e+00 1.43e+02 angle pdb=" O5' DG J 40 " pdb=" C5' DG J 40 " pdb=" C4' DG J 40 " ideal model delta sigma weight residual 109.40 118.81 -9.41 8.00e-01 1.56e+00 1.38e+02 angle pdb=" O5' DC J 74 " pdb=" C5' DC J 74 " pdb=" C4' DC J 74 " ideal model delta sigma weight residual 109.40 118.41 -9.01 8.00e-01 1.56e+00 1.27e+02 angle pdb=" O5' DG J 36 " pdb=" C5' DG J 36 " pdb=" C4' DG J 36 " ideal model delta sigma weight residual 109.40 118.32 -8.92 8.00e-01 1.56e+00 1.24e+02 angle pdb=" O5' DA I 136 " pdb=" C5' DA I 136 " pdb=" C4' DA I 136 " ideal model delta sigma weight residual 109.40 118.22 -8.82 8.00e-01 1.56e+00 1.22e+02 ... (remaining 27297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 9411 33.54 - 67.08: 1425 67.08 - 100.61: 73 100.61 - 134.15: 0 134.15 - 167.69: 1 Dihedral angle restraints: 10910 sinusoidal: 6386 harmonic: 4524 Sorted by residual: dihedral pdb=" CA VAL D 98 " pdb=" C VAL D 98 " pdb=" N ARG D 99 " pdb=" CA ARG D 99 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP E 106 " pdb=" C ASP E 106 " pdb=" N THR E 107 " pdb=" CA THR E 107 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA THR D 119 " pdb=" C THR D 119 " pdb=" N LYS D 120 " pdb=" CA LYS D 120 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 10907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2290 0.110 - 0.221: 656 0.221 - 0.331: 88 0.331 - 0.441: 17 0.441 - 0.552: 7 Chirality restraints: 3058 Sorted by residual: chirality pdb=" CA ARG C 17 " pdb=" N ARG C 17 " pdb=" C ARG C 17 " pdb=" CB ARG C 17 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" C3' DT J 41 " pdb=" C4' DT J 41 " pdb=" O3' DT J 41 " pdb=" C2' DT J 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.59e+00 ... (remaining 3055 not shown) Planarity restraints: 2471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 7 " -0.321 2.00e-02 2.50e+03 1.34e-01 4.94e+02 pdb=" N9 DA I 7 " 0.071 2.00e-02 2.50e+03 pdb=" C8 DA I 7 " 0.096 2.00e-02 2.50e+03 pdb=" N7 DA I 7 " 0.078 2.00e-02 2.50e+03 pdb=" C5 DA I 7 " 0.066 2.00e-02 2.50e+03 pdb=" C6 DA I 7 " -0.034 2.00e-02 2.50e+03 pdb=" N6 DA I 7 " -0.211 2.00e-02 2.50e+03 pdb=" N1 DA I 7 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DA I 7 " 0.065 2.00e-02 2.50e+03 pdb=" N3 DA I 7 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DA I 7 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 65 " 0.301 2.00e-02 2.50e+03 1.22e-01 4.46e+02 pdb=" N9 DG J 65 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG J 65 " -0.134 2.00e-02 2.50e+03 pdb=" N7 DG J 65 " -0.109 2.00e-02 2.50e+03 pdb=" C5 DG J 65 " -0.041 2.00e-02 2.50e+03 pdb=" C6 DG J 65 " 0.062 2.00e-02 2.50e+03 pdb=" O6 DG J 65 " 0.161 2.00e-02 2.50e+03 pdb=" N1 DG J 65 " 0.067 2.00e-02 2.50e+03 pdb=" C2 DG J 65 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DG J 65 " -0.091 2.00e-02 2.50e+03 pdb=" N3 DG J 65 " -0.071 2.00e-02 2.50e+03 pdb=" C4 DG J 65 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 69 " 0.238 2.00e-02 2.50e+03 1.19e-01 4.27e+02 pdb=" N9 DG J 69 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DG J 69 " -0.135 2.00e-02 2.50e+03 pdb=" N7 DG J 69 " -0.161 2.00e-02 2.50e+03 pdb=" C5 DG J 69 " -0.055 2.00e-02 2.50e+03 pdb=" C6 DG J 69 " 0.031 2.00e-02 2.50e+03 pdb=" O6 DG J 69 " 0.230 2.00e-02 2.50e+03 pdb=" N1 DG J 69 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG J 69 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DG J 69 " -0.107 2.00e-02 2.50e+03 pdb=" N3 DG J 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 69 " -0.020 2.00e-02 2.50e+03 ... (remaining 2468 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 8694 3.02 - 3.49: 19152 3.49 - 3.96: 31674 3.96 - 4.43: 36748 4.43 - 4.90: 52274 Nonbonded interactions: 148542 Sorted by model distance: nonbonded pdb=" OG1 THR B 82 " pdb=" OD2 ASP B 85 " model vdw 2.546 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.546 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.551 3.040 nonbonded pdb=" OG SER K 393 " pdb=" OE2 GLU K 402 " model vdw 2.553 3.040 nonbonded pdb=" OG SER K 272 " pdb=" OE2 GLU K 373 " model vdw 2.554 3.040 ... (remaining 148537 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = (chain 'G' and (resid 10 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)))) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 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 : 0.014 0.247 19318 Z= 1.199 Angle : 2.042 13.611 27305 Z= 1.851 Chirality : 0.104 0.552 3058 Planarity : 0.029 0.248 2471 Dihedral : 24.893 167.691 7988 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 1.24 % Allowed : 6.58 % Favored : 92.19 % Rotamer: Outliers : 5.22 % Allowed : 10.67 % Favored : 84.10 % Cbeta Deviations : 1.30 % 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 are not related in a simple way. whole: -2.98 (0.19), residues: 1536 helix: -2.30 (0.16), residues: 733 sheet: -0.60 (0.48), residues: 111 loop : -1.69 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG F 45 TYR 0.200 0.029 TYR C 57 PHE 0.071 0.013 PHE L 150 TRP 0.059 0.015 TRP K 455 HIS 0.022 0.004 HIS L 310 Details of bonding type rmsd/Z covalent geometry : bond 0.01352 / 1.20 (19314) covalent geometry : angle 2.04067 / 1.85 (27302) hydrogen bonds : bond 0.19480 / 12.36 ( 926) hydrogen bonds : angle 7.85497 / 5.60 ( 2343) metal coordination : bond 0.15921 / 8.14 ( 4) metal coordination : angle 8.22331 / 4.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 0.555 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: A 79 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7351 (tttm) REVERT: A 133 GLU cc_start: 0.4406 (OUTLIER) cc_final: 0.4149 (mt-10) REVERT: B 63 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: B 91 LYS cc_start: 0.8072 (tptp) cc_final: 0.7810 (mmmm) REVERT: C 24 GLN cc_start: 0.5717 (OUTLIER) cc_final: 0.5385 (mp10) REVERT: C 73 ASN cc_start: 0.7941 (t0) cc_final: 0.7353 (m-40) REVERT: D 83 TYR cc_start: 0.3155 (m-10) cc_final: 0.2022 (t80) REVERT: D 89 ILE cc_start: 0.6564 (pt) cc_final: 0.6138 (pt) REVERT: D 120 LYS cc_start: 0.6674 (ptpp) cc_final: 0.6314 (ptmm) REVERT: E 81 ASP cc_start: 0.8450 (m-30) cc_final: 0.7975 (t0) REVERT: E 120 MET cc_start: 0.7017 (ptp) cc_final: 0.6464 (ptt) REVERT: E 129 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6590 (tpt90) REVERT: F 74 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7984 (mt-10) REVERT: G 63 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6665 (mm) REVERT: G 72 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8680 (p0) REVERT: H 105 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6205 (mm-30) REVERT: N 56 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7151 (t) outliers start: 70 outliers final: 18 residues processed: 246 average time/residue: 0.1392 time to fit residues: 49.4056 Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 427 LYS Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 68 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 GLN K 419 GLN ** L 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.079155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.065957 restraints weight = 127208.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065771 restraints weight = 100201.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.065791 restraints weight = 83570.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065887 restraints weight = 79117.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065847 restraints weight = 76953.502| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19318 Z= 0.224 Angle : 0.993 12.027 27305 Z= 0.537 Chirality : 0.064 0.381 3058 Planarity : 0.006 0.062 2471 Dihedral : 28.795 179.704 4942 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.88 % Rotamer: Outliers : 3.81 % Allowed : 15.30 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.20), residues: 1536 helix: -1.24 (0.17), residues: 731 sheet: -0.96 (0.41), residues: 136 loop : -1.44 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 179 TYR 0.029 0.003 TYR L 279 PHE 0.021 0.002 PHE N 62 TRP 0.025 0.002 TRP L 193 HIS 0.023 0.002 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 (19314) covalent geometry : angle 0.99278 / 0.54 (27302) hydrogen bonds : bond 0.08515 / 5.51 ( 926) hydrogen bonds : angle 5.28683 / 3.76 ( 2343) metal coordination : bond 0.01266 / 0.65 ( 4) metal coordination : angle 1.72101 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.575 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: B 93 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: C 24 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5679 (mp10) REVERT: D 62 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.5755 (mmm) REVERT: D 83 TYR cc_start: 0.3470 (m-10) cc_final: 0.2313 (t80) REVERT: G 63 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8807 (mm) REVERT: G 101 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (p) REVERT: M 38 THR cc_start: 0.8728 (m) cc_final: 0.8434 (p) REVERT: N 2 ASP cc_start: 0.7842 (m-30) cc_final: 0.7554 (m-30) REVERT: N 25 PHE cc_start: 0.7587 (m-80) cc_final: 0.7247 (m-80) REVERT: N 70 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: N 99 LEU cc_start: 0.8237 (mp) cc_final: 0.7821 (mt) outliers start: 51 outliers final: 26 residues processed: 173 average time/residue: 0.1301 time to fit residues: 33.4856 Evaluate side-chains 143 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 97 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 110 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN L 278 GLN ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.080139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066940 restraints weight = 128753.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.066804 restraints weight = 98332.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.066709 restraints weight = 90063.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.066807 restraints weight = 84988.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.066846 restraints weight = 76226.980| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19318 Z= 0.170 Angle : 0.807 9.055 27305 Z= 0.449 Chirality : 0.054 0.382 3058 Planarity : 0.005 0.059 2471 Dihedral : 28.712 173.964 4916 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.51 % Allowed : 17.16 % Favored : 79.33 % 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 are not related in a simple way. whole: -1.49 (0.21), residues: 1536 helix: -0.61 (0.19), residues: 723 sheet: -0.64 (0.41), residues: 130 loop : -1.37 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 33 TYR 0.027 0.002 TYR M 76 PHE 0.029 0.002 PHE N 4 TRP 0.018 0.001 TRP L 193 HIS 0.020 0.001 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (19314) covalent geometry : angle 0.80715 / 0.45 (27302) hydrogen bonds : bond 0.06745 / 4.38 ( 926) hydrogen bonds : angle 4.71099 / 3.31 ( 2343) metal coordination : bond 0.00774 / 0.40 ( 4) metal coordination : angle 1.76481 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: C 24 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5881 (mp10) REVERT: C 64 GLU cc_start: 0.1256 (OUTLIER) cc_final: 0.0621 (pt0) REVERT: D 68 ASP cc_start: 0.6033 (t0) cc_final: 0.5796 (t0) REVERT: D 83 TYR cc_start: 0.3213 (m-10) cc_final: 0.2343 (t80) REVERT: G 63 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8758 (mm) REVERT: L 129 MET cc_start: 0.7928 (mmm) cc_final: 0.7378 (mmm) REVERT: L 165 MET cc_start: 0.7482 (pmm) cc_final: 0.5518 (pmm) REVERT: L 278 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6003 (pp30) REVERT: M 27 HIS cc_start: 0.7418 (m90) cc_final: 0.6960 (m90) REVERT: M 30 ILE cc_start: 0.4228 (OUTLIER) cc_final: 0.3887 (tp) REVERT: M 38 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8736 (p) REVERT: M 110 LEU cc_start: 0.9251 (mm) cc_final: 0.8994 (tp) REVERT: N 6 MET cc_start: 0.6234 (tmm) cc_final: 0.5243 (tpp) REVERT: N 25 PHE cc_start: 0.7397 (m-80) cc_final: 0.6807 (m-80) REVERT: N 70 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: N 95 SER cc_start: 0.9064 (m) cc_final: 0.8783 (t) outliers start: 47 outliers final: 16 residues processed: 166 average time/residue: 0.1168 time to fit residues: 30.0675 Evaluate side-chains 129 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 278 GLN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 150 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 178 optimal weight: 0.0980 chunk 32 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.065957 restraints weight = 128574.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.065909 restraints weight = 101627.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.065841 restraints weight = 84640.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.065953 restraints weight = 78256.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.065938 restraints weight = 73542.372| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19318 Z= 0.182 Angle : 0.785 8.849 27305 Z= 0.432 Chirality : 0.053 0.357 3058 Planarity : 0.005 0.066 2471 Dihedral : 28.647 172.476 4903 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 3.43 % Allowed : 18.81 % Favored : 77.76 % 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 are not related in a simple way. whole: -1.41 (0.21), residues: 1536 helix: -0.52 (0.19), residues: 719 sheet: -0.55 (0.42), residues: 126 loop : -1.38 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 68 TYR 0.037 0.002 TYR M 76 PHE 0.013 0.002 PHE N 4 TRP 0.015 0.001 TRP L 193 HIS 0.015 0.001 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (19314) covalent geometry : angle 0.78438 / 0.43 (27302) hydrogen bonds : bond 0.06623 / 4.26 ( 926) hydrogen bonds : angle 4.59540 / 3.22 ( 2343) metal coordination : bond 0.00373 / 0.19 ( 4) metal coordination : angle 1.97362 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.378 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: B 93 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: C 24 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5780 (mp10) REVERT: C 116 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8489 (pp) REVERT: D 68 ASP cc_start: 0.5892 (t0) cc_final: 0.5668 (t0) REVERT: D 83 TYR cc_start: 0.3256 (m-10) cc_final: 0.2605 (t80) REVERT: F 91 LYS cc_start: 0.8592 (pptt) cc_final: 0.8224 (pptt) REVERT: L 129 MET cc_start: 0.7883 (mmm) cc_final: 0.7578 (mmm) REVERT: M 17 MET cc_start: 0.8241 (ptt) cc_final: 0.8012 (pmm) REVERT: M 27 HIS cc_start: 0.7664 (m90) cc_final: 0.7153 (m90) REVERT: M 38 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8836 (p) REVERT: M 110 LEU cc_start: 0.9316 (mm) cc_final: 0.9035 (tp) REVERT: N 6 MET cc_start: 0.6316 (tmm) cc_final: 0.5485 (tpp) REVERT: N 25 PHE cc_start: 0.7525 (m-80) cc_final: 0.6831 (m-80) REVERT: N 70 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: N 95 SER cc_start: 0.9080 (m) cc_final: 0.8862 (t) REVERT: N 103 MET cc_start: 0.7393 (mmp) cc_final: 0.7087 (mmm) outliers start: 46 outliers final: 29 residues processed: 152 average time/residue: 0.1216 time to fit residues: 28.4632 Evaluate side-chains 134 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 97 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 98 optimal weight: 40.0000 chunk 13 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.080403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.067242 restraints weight = 127169.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066878 restraints weight = 97921.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.066744 restraints weight = 92725.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.066798 restraints weight = 90086.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066831 restraints weight = 79182.690| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19318 Z= 0.149 Angle : 0.720 11.777 27305 Z= 0.398 Chirality : 0.048 0.340 3058 Planarity : 0.004 0.039 2471 Dihedral : 28.441 172.308 4903 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 3.73 % Allowed : 18.81 % Favored : 77.46 % 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 are not related in a simple way. whole: -1.11 (0.21), residues: 1536 helix: -0.20 (0.20), residues: 723 sheet: -0.37 (0.43), residues: 126 loop : -1.32 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 82 TYR 0.034 0.002 TYR M 76 PHE 0.022 0.001 PHE M 109 TRP 0.013 0.001 TRP L 193 HIS 0.016 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (19314) covalent geometry : angle 0.71939 / 0.40 (27302) hydrogen bonds : bond 0.05508 / 3.56 ( 926) hydrogen bonds : angle 4.38212 / 3.08 ( 2343) metal coordination : bond 0.00422 / 0.22 ( 4) metal coordination : angle 1.94314 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: C 24 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: C 64 GLU cc_start: 0.1617 (OUTLIER) cc_final: 0.1210 (pt0) REVERT: C 84 GLN cc_start: 0.5287 (OUTLIER) cc_final: 0.5060 (tt0) REVERT: C 116 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8450 (pp) REVERT: D 79 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7223 (mtp180) REVERT: E 65 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7959 (mt) REVERT: G 63 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8759 (mm) REVERT: H 99 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6797 (ttp-170) REVERT: K 277 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8432 (mm) REVERT: L 129 MET cc_start: 0.7471 (mmm) cc_final: 0.6506 (mmm) REVERT: M 27 HIS cc_start: 0.7586 (m90) cc_final: 0.7051 (m90) REVERT: M 30 ILE cc_start: 0.3986 (OUTLIER) cc_final: 0.3758 (tp) REVERT: M 38 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8777 (p) REVERT: M 110 LEU cc_start: 0.9290 (mm) cc_final: 0.9001 (tp) REVERT: N 6 MET cc_start: 0.6512 (tmm) cc_final: 0.5757 (tpp) REVERT: N 25 PHE cc_start: 0.7452 (m-80) cc_final: 0.6813 (m-80) REVERT: N 95 SER cc_start: 0.9094 (m) cc_final: 0.8871 (t) outliers start: 50 outliers final: 25 residues processed: 162 average time/residue: 0.1175 time to fit residues: 29.1923 Evaluate side-chains 137 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain K residue 454 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 114 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 24 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN L 249 ASN ** N 49 GLN ** 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 = 0.4027 r_free = 0.4027 target = 0.079275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065644 restraints weight = 126789.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.065300 restraints weight = 101376.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.065314 restraints weight = 87877.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.065379 restraints weight = 81362.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.065375 restraints weight = 77832.716| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19318 Z= 0.203 Angle : 0.777 15.120 27305 Z= 0.422 Chirality : 0.051 0.343 3058 Planarity : 0.005 0.092 2471 Dihedral : 28.511 175.367 4903 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.53 % Favored : 94.27 % Rotamer: Outliers : 4.63 % Allowed : 19.03 % Favored : 76.34 % 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 are not related in a simple way. whole: -1.40 (0.21), residues: 1536 helix: -0.46 (0.19), residues: 732 sheet: -0.43 (0.43), residues: 123 loop : -1.46 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 82 TYR 0.028 0.002 TYR M 76 PHE 0.016 0.002 PHE H 70 TRP 0.014 0.001 TRP L 193 HIS 0.010 0.002 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (19314) covalent geometry : angle 0.77641 / 0.42 (27302) hydrogen bonds : bond 0.06455 / 4.16 ( 926) hydrogen bonds : angle 4.52222 / 3.16 ( 2343) metal coordination : bond 0.00386 / 0.19 ( 4) metal coordination : angle 1.85156 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 0.513 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: B 84 MET cc_start: 0.7376 (mmm) cc_final: 0.7163 (mmm) REVERT: B 93 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: C 24 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5743 (mp10) REVERT: C 116 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8474 (pp) REVERT: D 100 LEU cc_start: 0.5999 (pp) cc_final: 0.5685 (pt) REVERT: E 65 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8069 (mt) REVERT: H 99 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7010 (ttp-170) REVERT: K 277 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (mm) REVERT: L 129 MET cc_start: 0.7436 (mmm) cc_final: 0.6600 (mmm) REVERT: M 27 HIS cc_start: 0.7498 (m90) cc_final: 0.7017 (m90) REVERT: M 30 ILE cc_start: 0.3991 (OUTLIER) cc_final: 0.3756 (tp) REVERT: M 110 LEU cc_start: 0.9306 (mm) cc_final: 0.9004 (tp) REVERT: N 6 MET cc_start: 0.6522 (tmm) cc_final: 0.5790 (tpp) REVERT: N 25 PHE cc_start: 0.7516 (m-80) cc_final: 0.6847 (m-80) REVERT: N 95 SER cc_start: 0.9081 (m) cc_final: 0.8869 (t) outliers start: 62 outliers final: 41 residues processed: 161 average time/residue: 0.1266 time to fit residues: 31.4387 Evaluate side-chains 149 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 176 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.079541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.065895 restraints weight = 127649.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065921 restraints weight = 98383.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.065709 restraints weight = 87230.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065813 restraints weight = 84471.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.065898 restraints weight = 73894.248| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19318 Z= 0.163 Angle : 0.734 12.399 27305 Z= 0.401 Chirality : 0.048 0.326 3058 Planarity : 0.004 0.043 2471 Dihedral : 28.456 176.860 4903 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.60 % Rotamer: Outliers : 4.10 % Allowed : 19.78 % Favored : 76.12 % 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 are not related in a simple way. whole: -1.29 (0.21), residues: 1536 helix: -0.32 (0.19), residues: 733 sheet: -0.41 (0.43), residues: 123 loop : -1.46 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 82 TYR 0.031 0.002 TYR M 76 PHE 0.022 0.001 PHE M 109 TRP 0.013 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (19314) covalent geometry : angle 0.73387 / 0.40 (27302) hydrogen bonds : bond 0.05886 / 3.80 ( 926) hydrogen bonds : angle 4.41520 / 3.10 ( 2343) metal coordination : bond 0.00373 / 0.19 ( 4) metal coordination : angle 1.82832 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 0.465 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: B 84 MET cc_start: 0.7444 (mmm) cc_final: 0.7236 (mmm) REVERT: B 93 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: C 24 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: C 116 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8467 (pp) REVERT: D 62 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5541 (mmm) REVERT: D 79 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7063 (mtp180) REVERT: D 100 LEU cc_start: 0.6086 (pp) cc_final: 0.5789 (pt) REVERT: D 120 LYS cc_start: 0.7127 (ptpp) cc_final: 0.6779 (ptmm) REVERT: E 65 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8125 (mt) REVERT: E 79 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7244 (ttmt) REVERT: G 96 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8342 (tp) REVERT: H 99 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6884 (ttp-170) REVERT: K 277 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8236 (mm) REVERT: L 129 MET cc_start: 0.7595 (mmm) cc_final: 0.6918 (mmm) REVERT: M 27 HIS cc_start: 0.7405 (m90) cc_final: 0.6971 (m90) REVERT: M 30 ILE cc_start: 0.3980 (OUTLIER) cc_final: 0.3737 (tp) REVERT: M 110 LEU cc_start: 0.9264 (mm) cc_final: 0.8977 (tp) REVERT: N 6 MET cc_start: 0.6511 (tmm) cc_final: 0.5815 (tpp) REVERT: N 25 PHE cc_start: 0.7538 (m-80) cc_final: 0.6865 (m-80) REVERT: N 95 SER cc_start: 0.9062 (m) cc_final: 0.8853 (t) outliers start: 55 outliers final: 33 residues processed: 155 average time/residue: 0.1224 time to fit residues: 29.2477 Evaluate side-chains 145 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 70 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 82 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.079430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.065489 restraints weight = 127114.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.065122 restraints weight = 104071.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.065238 restraints weight = 89773.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.065332 restraints weight = 78407.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.065324 restraints weight = 74432.392| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19318 Z= 0.159 Angle : 0.723 10.980 27305 Z= 0.394 Chirality : 0.047 0.322 3058 Planarity : 0.004 0.039 2471 Dihedral : 28.413 179.346 4901 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.73 % Favored : 94.08 % Rotamer: Outliers : 3.58 % Allowed : 20.67 % Favored : 75.75 % 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 are not related in a simple way. whole: -1.20 (0.21), residues: 1536 helix: -0.24 (0.19), residues: 732 sheet: -0.30 (0.43), residues: 126 loop : -1.44 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 68 TYR 0.024 0.002 TYR M 76 PHE 0.013 0.001 PHE K 357 TRP 0.012 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (19314) covalent geometry : angle 0.72239 / 0.39 (27302) hydrogen bonds : bond 0.05709 / 3.70 ( 926) hydrogen bonds : angle 4.39844 / 3.08 ( 2343) metal coordination : bond 0.00409 / 0.21 ( 4) metal coordination : angle 1.75522 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: C 24 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.5570 (mp10) REVERT: C 116 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8456 (pp) REVERT: D 62 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5560 (mmm) REVERT: D 79 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7168 (mtp180) REVERT: D 100 LEU cc_start: 0.6289 (pp) cc_final: 0.6018 (pt) REVERT: D 120 LYS cc_start: 0.7084 (ptpp) cc_final: 0.6756 (ptmm) REVERT: E 56 LYS cc_start: 0.7350 (mmmm) cc_final: 0.7134 (ttmm) REVERT: E 65 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8019 (mt) REVERT: G 96 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8390 (tp) REVERT: H 99 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6962 (ttp-170) REVERT: L 129 MET cc_start: 0.7774 (mmm) cc_final: 0.7150 (mmm) REVERT: M 27 HIS cc_start: 0.7591 (m90) cc_final: 0.7087 (m90) REVERT: M 30 ILE cc_start: 0.4218 (OUTLIER) cc_final: 0.3960 (tp) REVERT: M 110 LEU cc_start: 0.9316 (mm) cc_final: 0.9026 (tp) REVERT: N 6 MET cc_start: 0.6525 (tmm) cc_final: 0.5840 (tpp) REVERT: N 25 PHE cc_start: 0.7853 (m-80) cc_final: 0.7198 (m-80) REVERT: N 95 SER cc_start: 0.9162 (m) cc_final: 0.8953 (t) outliers start: 48 outliers final: 36 residues processed: 149 average time/residue: 0.1177 time to fit residues: 27.0491 Evaluate side-chains 142 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 280 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 4 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 172 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 111 optimal weight: 0.0040 chunk 135 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 chunk 93 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 287 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.079309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065615 restraints weight = 126441.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.065637 restraints weight = 102141.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.065555 restraints weight = 88481.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.065569 restraints weight = 91499.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065563 restraints weight = 82056.970| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19318 Z= 0.167 Angle : 0.732 13.677 27305 Z= 0.396 Chirality : 0.047 0.318 3058 Planarity : 0.004 0.043 2471 Dihedral : 28.399 178.418 4901 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.99 % Favored : 93.82 % Rotamer: Outliers : 3.51 % Allowed : 21.19 % Favored : 75.30 % 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 are not related in a simple way. whole: -1.23 (0.21), residues: 1536 helix: -0.28 (0.19), residues: 734 sheet: -0.15 (0.45), residues: 123 loop : -1.48 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 68 TYR 0.024 0.002 TYR M 76 PHE 0.021 0.001 PHE M 77 TRP 0.012 0.001 TRP L 193 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (19314) covalent geometry : angle 0.73193 / 0.40 (27302) hydrogen bonds : bond 0.05825 / 3.77 ( 926) hydrogen bonds : angle 4.41435 / 3.09 ( 2343) metal coordination : bond 0.00400 / 0.20 ( 4) metal coordination : angle 1.79937 / 1.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6859 (mp10) REVERT: C 24 GLN cc_start: 0.5999 (OUTLIER) cc_final: 0.5568 (mp10) REVERT: C 116 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8525 (pp) REVERT: D 62 MET cc_start: 0.6326 (pmm) cc_final: 0.5614 (mmm) REVERT: D 79 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7161 (mtp180) REVERT: D 100 LEU cc_start: 0.6280 (pp) cc_final: 0.5970 (pt) REVERT: E 65 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (mt) REVERT: H 99 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6976 (ttp-170) REVERT: L 129 MET cc_start: 0.7673 (mmm) cc_final: 0.7101 (mmm) REVERT: M 27 HIS cc_start: 0.7378 (m90) cc_final: 0.6958 (m90) REVERT: M 30 ILE cc_start: 0.3942 (OUTLIER) cc_final: 0.3691 (tp) REVERT: M 110 LEU cc_start: 0.9231 (mm) cc_final: 0.8975 (tp) REVERT: N 6 MET cc_start: 0.6506 (tmm) cc_final: 0.5835 (tpp) REVERT: N 25 PHE cc_start: 0.7674 (m-80) cc_final: 0.7043 (m-80) REVERT: N 95 SER cc_start: 0.9037 (m) cc_final: 0.8816 (t) outliers start: 47 outliers final: 36 residues processed: 146 average time/residue: 0.1275 time to fit residues: 28.2253 Evaluate side-chains 139 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 178 optimal weight: 0.0170 chunk 134 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.080171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.066806 restraints weight = 127235.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.066788 restraints weight = 105743.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066791 restraints weight = 84531.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.066864 restraints weight = 84953.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.066838 restraints weight = 78639.407| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19318 Z= 0.139 Angle : 0.709 12.250 27305 Z= 0.385 Chirality : 0.045 0.311 3058 Planarity : 0.004 0.037 2471 Dihedral : 28.251 177.875 4898 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.88 % Favored : 94.92 % Rotamer: Outliers : 2.16 % Allowed : 22.61 % Favored : 75.22 % 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 are not related in a simple way. whole: -1.00 (0.21), residues: 1536 helix: -0.05 (0.20), residues: 730 sheet: -0.03 (0.44), residues: 123 loop : -1.42 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 68 TYR 0.024 0.002 TYR M 76 PHE 0.013 0.001 PHE K 357 TRP 0.009 0.001 TRP L 193 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (19314) covalent geometry : angle 0.70831 / 0.39 (27302) hydrogen bonds : bond 0.05033 / 3.27 ( 926) hydrogen bonds : angle 4.26213 / 2.98 ( 2343) metal coordination : bond 0.00710 / 0.37 ( 4) metal coordination : angle 1.72560 / 1.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: C 24 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.5543 (mp10) REVERT: C 64 GLU cc_start: 0.1969 (OUTLIER) cc_final: 0.1443 (pt0) REVERT: C 84 GLN cc_start: 0.5294 (OUTLIER) cc_final: 0.5077 (tt0) REVERT: C 116 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 117 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7374 (Cg_endo) REVERT: D 62 MET cc_start: 0.6238 (pmm) cc_final: 0.5528 (mmm) REVERT: D 79 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7183 (mtp180) REVERT: D 100 LEU cc_start: 0.6245 (pp) cc_final: 0.6010 (pt) REVERT: E 79 LYS cc_start: 0.7582 (ttmt) cc_final: 0.7365 (ttmt) REVERT: G 63 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8782 (mm) REVERT: H 99 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6969 (ttp-170) REVERT: L 129 MET cc_start: 0.7490 (mmm) cc_final: 0.6996 (mmm) REVERT: L 286 ARG cc_start: 0.7331 (tpt170) cc_final: 0.6468 (tpp-160) REVERT: M 27 HIS cc_start: 0.7228 (m90) cc_final: 0.6864 (m90) REVERT: M 110 LEU cc_start: 0.9167 (mm) cc_final: 0.8928 (tp) REVERT: N 6 MET cc_start: 0.6505 (tmm) cc_final: 0.5846 (tpp) REVERT: N 25 PHE cc_start: 0.7531 (m-80) cc_final: 0.6905 (m-80) REVERT: N 68 ARG cc_start: 0.8241 (mmm160) cc_final: 0.8011 (mmp80) outliers start: 29 outliers final: 17 residues processed: 136 average time/residue: 0.1569 time to fit residues: 32.3336 Evaluate side-chains 127 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain M residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 105 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 43 optimal weight: 7.9990 chunk 76 optimal weight: 40.0000 chunk 13 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.079212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.065670 restraints weight = 127020.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065552 restraints weight = 100699.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.065571 restraints weight = 83936.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.065670 restraints weight = 80174.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065635 restraints weight = 75160.962| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19318 Z= 0.189 Angle : 0.751 12.346 27305 Z= 0.404 Chirality : 0.048 0.319 3058 Planarity : 0.005 0.048 2471 Dihedral : 28.353 175.514 4896 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.12 % Favored : 93.68 % Rotamer: Outliers : 2.24 % Allowed : 22.61 % Favored : 75.15 % 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 are not related in a simple way. whole: -1.22 (0.21), residues: 1536 helix: -0.29 (0.19), residues: 734 sheet: -0.08 (0.44), residues: 125 loop : -1.46 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.029 0.002 TYR F 88 PHE 0.038 0.002 PHE M 109 TRP 0.013 0.001 TRP L 193 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (19314) covalent geometry : angle 0.75069 / 0.40 (27302) hydrogen bonds : bond 0.06091 / 3.95 ( 926) hydrogen bonds : angle 4.41247 / 3.07 ( 2343) metal coordination : bond 0.00398 / 0.20 ( 4) metal coordination : angle 1.68619 / 0.94 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.60 seconds wall clock time: 46 minutes 47.71 seconds (2807.71 seconds total)