Starting phenix.real_space_refine on Sat Oct 11 21:42:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol1_16936/10_2025/8ol1_16936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol1_16936/10_2025/8ol1_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_16936/10_2025/8ol1_16936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol1_16936/10_2025/8ol1_16936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ol1_16936/10_2025/8ol1_16936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol1_16936/10_2025/8ol1_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-2.0-5842/lib/python3.9/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: 4.33, per 1000 atoms: 0.24 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: 1.62 Conformation dependent library (CDL) restraints added in 544.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.65 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: 4.00 Time building geometry restraints manager: 2.08 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=" CA PRO N 96 " pdb=" C PRO N 96 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.38e+01 bond pdb=" CZ ARG K 236 " pdb=" NH2 ARG K 236 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" CZ ARG K 255 " pdb=" NH2 ARG K 255 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" CA GLN D 47 " pdb=" C GLN D 47 " ideal model delta sigma weight residual 1.523 1.569 -0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" CZ ARG A 40 " pdb=" NH2 ARG A 40 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.19e+01 ... (remaining 19309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 18545 1.91 - 3.82: 6998 3.82 - 5.73: 1565 5.73 - 7.63: 177 7.63 - 9.54: 17 Bond angle restraints: 27302 Sorted by residual: angle pdb=" CA PHE F 61 " pdb=" CB PHE F 61 " pdb=" CG PHE F 61 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 angle pdb=" CA HIS K 217 " pdb=" CB HIS K 217 " pdb=" CG HIS K 217 " ideal model delta sigma weight residual 113.80 107.58 6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CA ASP K 520 " pdb=" CB ASP K 520 " pdb=" CG ASP K 520 " ideal model delta sigma weight residual 112.60 118.54 -5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" C LYS D 46 " pdb=" N GLN D 47 " pdb=" CA GLN D 47 " ideal model delta sigma weight residual 120.28 128.23 -7.95 1.34e+00 5.57e-01 3.52e+01 angle pdb=" C THR D 52 " pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 121.82 126.76 -4.94 8.40e-01 1.42e+00 3.45e+01 ... (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: 2331 0.110 - 0.221: 616 0.221 - 0.331: 87 0.331 - 0.441: 18 0.441 - 0.552: 6 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=" CA GLN G 104 " pdb=" N GLN G 104 " pdb=" C GLN G 104 " pdb=" CB GLN G 104 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.120 Find NCS groups from input model: 0.230 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 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= 0.774 Angle : 2.025 13.611 27305 Z= 1.327 Chirality : 0.102 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 aren 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 covalent geometry : bond 0.01332 (19314) covalent geometry : angle 2.02289 (27302) hydrogen bonds : bond 0.19480 ( 926) hydrogen bonds : angle 7.85497 ( 2343) metal coordination : bond 0.15921 ( 4) metal coordination : angle 8.22331 ( 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 : 0.526 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: 0.6139 (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: 0.1758 time to fit residues: 61.6562 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 : 0.597 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 68 ASN D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN K 371 GLN K 419 GLN K 429 HIS L 278 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.080009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066895 restraints weight = 128227.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.066640 restraints weight = 106943.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066822 restraints weight = 88895.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.066813 restraints weight = 86102.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066824 restraints weight = 83208.235| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2895 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= 0.195 Angle : 0.792 11.308 27305 Z= 0.445 Chirality : 0.045 0.297 3058 Planarity : 0.005 0.042 2471 Dihedral : 28.630 178.734 4942 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.69 % Favored : 94.99 % Rotamer: Outliers : 3.81 % Allowed : 14.70 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.20), residues: 1536 helix: -0.83 (0.18), residues: 730 sheet: -0.64 (0.42), residues: 133 loop : -1.25 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 251 TYR 0.027 0.002 TYR L 279 PHE 0.018 0.002 PHE N 93 TRP 0.021 0.002 TRP L 193 HIS 0.025 0.002 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00416 (19314) covalent geometry : angle 0.79160 (27302) hydrogen bonds : bond 0.06667 ( 926) hydrogen bonds : angle 4.82895 ( 2343) metal coordination : bond 0.02139 ( 4) metal coordination : angle 2.67121 ( 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 185 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.672 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: B 93 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: C 24 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5591 (mp10) REVERT: D 79 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7150 (mtp-110) REVERT: D 83 TYR cc_start: 0.3234 (m-10) cc_final: 0.2835 (t80) REVERT: G 63 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8764 (mm) REVERT: M 27 HIS cc_start: 0.7451 (m170) cc_final: 0.7044 (m90) REVERT: M 30 ILE cc_start: 0.3501 (OUTLIER) cc_final: 0.3247 (tp) REVERT: M 38 THR cc_start: 0.8515 (m) cc_final: 0.8264 (p) REVERT: N 2 ASP cc_start: 0.7343 (m-30) cc_final: 0.7004 (m-30) REVERT: N 6 MET cc_start: 0.6117 (tmm) cc_final: 0.5426 (tpp) REVERT: N 25 PHE cc_start: 0.7339 (m-80) cc_final: 0.6731 (m-80) REVERT: N 99 LEU cc_start: 0.8035 (mp) cc_final: 0.7463 (mt) outliers start: 51 outliers final: 21 residues processed: 180 average time/residue: 0.1714 time to fit residues: 45.2763 Evaluate side-chains 139 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 24 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 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE 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 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 M residue 30 ILE Chi-restraints excluded: chain N residue 68 ARG 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: 0.9990 chunk 165 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN L 278 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.080339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066915 restraints weight = 129433.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.066772 restraints weight = 100100.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066746 restraints weight = 84532.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.066842 restraints weight = 78996.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.066877 restraints weight = 73500.683| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19318 Z= 0.163 Angle : 0.697 13.502 27305 Z= 0.389 Chirality : 0.041 0.225 3058 Planarity : 0.005 0.129 2471 Dihedral : 28.098 179.293 4914 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 3.28 % Allowed : 15.90 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1536 helix: -0.25 (0.19), residues: 726 sheet: -0.40 (0.42), residues: 132 loop : -1.17 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 33 TYR 0.015 0.002 TYR D 42 PHE 0.014 0.001 PHE K 265 TRP 0.017 0.001 TRP L 193 HIS 0.019 0.001 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00345 (19314) covalent geometry : angle 0.69635 (27302) hydrogen bonds : bond 0.05301 ( 926) hydrogen bonds : angle 4.34732 ( 2343) metal coordination : bond 0.00502 ( 4) metal coordination : angle 1.88678 ( 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 169 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.645 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: 0.7592 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: C 24 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5357 (mp10) REVERT: D 62 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5641 (mmm) REVERT: D 79 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7183 (mtp180) REVERT: G 63 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8766 (mm) REVERT: L 278 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.5966 (pm20) REVERT: M 27 HIS cc_start: 0.7963 (m170) cc_final: 0.7561 (m90) REVERT: M 30 ILE cc_start: 0.4230 (OUTLIER) cc_final: 0.3862 (tp) REVERT: M 38 THR cc_start: 0.8922 (m) cc_final: 0.8698 (p) REVERT: N 1 MET cc_start: 0.8423 (tmm) cc_final: 0.8212 (tmm) REVERT: N 6 MET cc_start: 0.6505 (tmm) cc_final: 0.5718 (tpp) REVERT: N 25 PHE cc_start: 0.7418 (m-80) cc_final: 0.6793 (m-80) outliers start: 44 outliers final: 22 residues processed: 164 average time/residue: 0.1512 time to fit residues: 37.8278 Evaluate side-chains 136 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 89 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 91 LYS 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 H residue 101 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 454 GLN 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 278 GLN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain N residue 68 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 150 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 178 optimal weight: 0.0670 chunk 32 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.080002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.066436 restraints weight = 128781.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.066154 restraints weight = 96363.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.066378 restraints weight = 84328.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.066429 restraints weight = 75557.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.066378 restraints weight = 69310.218| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19318 Z= 0.167 Angle : 0.675 13.455 27305 Z= 0.375 Chirality : 0.040 0.224 3058 Planarity : 0.004 0.074 2471 Dihedral : 27.982 176.817 4911 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 3.81 % Allowed : 17.01 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.21), residues: 1536 helix: -0.13 (0.19), residues: 733 sheet: -0.46 (0.41), residues: 132 loop : -1.14 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 33 TYR 0.026 0.002 TYR M 76 PHE 0.014 0.001 PHE M 109 TRP 0.014 0.001 TRP L 193 HIS 0.017 0.002 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00361 (19314) covalent geometry : angle 0.67483 (27302) hydrogen bonds : bond 0.05232 ( 926) hydrogen bonds : angle 4.24631 ( 2343) metal coordination : bond 0.00360 ( 4) metal coordination : angle 2.01925 ( 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 174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.587 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: 0.7560 (OUTLIER) cc_final: 0.6708 (mp10) REVERT: C 24 GLN cc_start: 0.5627 (OUTLIER) cc_final: 0.5294 (mp10) REVERT: C 64 GLU cc_start: 0.1615 (OUTLIER) cc_final: 0.1130 (pt0) REVERT: D 59 MET cc_start: 0.6218 (tpp) cc_final: 0.5335 (tpp) REVERT: D 79 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7205 (mtp180) REVERT: M 27 HIS cc_start: 0.7948 (m170) cc_final: 0.7743 (m90) REVERT: M 30 ILE cc_start: 0.3570 (OUTLIER) cc_final: 0.3346 (tp) REVERT: M 77 PHE cc_start: 0.8817 (m-10) cc_final: 0.8335 (m-80) REVERT: M 79 TYR cc_start: 0.8251 (t80) cc_final: 0.7721 (t80) REVERT: M 80 LYS cc_start: 0.9030 (pttp) cc_final: 0.8638 (pttm) REVERT: M 83 TYR cc_start: 0.7311 (m-80) cc_final: 0.6970 (m-80) REVERT: N 6 MET cc_start: 0.6619 (tmm) cc_final: 0.6025 (tpp) REVERT: N 25 PHE cc_start: 0.7594 (m-80) cc_final: 0.6882 (m-80) REVERT: N 35 LEU cc_start: 0.7745 (tp) cc_final: 0.7499 (tt) outliers start: 51 outliers final: 28 residues processed: 165 average time/residue: 0.1515 time to fit residues: 38.1818 Evaluate side-chains 138 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 96 LEU 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 97 GLU 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 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 163 ASP 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 N residue 4 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 118 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.080951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.067847 restraints weight = 127511.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.067660 restraints weight = 98598.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.067486 restraints weight = 86718.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.067599 restraints weight = 83575.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067625 restraints weight = 76256.055| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19318 Z= 0.147 Angle : 0.645 11.594 27305 Z= 0.356 Chirality : 0.039 0.326 3058 Planarity : 0.004 0.053 2471 Dihedral : 27.747 174.978 4902 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 2.99 % Allowed : 17.84 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.21), residues: 1536 helix: 0.12 (0.20), residues: 736 sheet: -0.46 (0.41), residues: 138 loop : -1.14 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 82 TYR 0.026 0.002 TYR M 76 PHE 0.012 0.001 PHE K 357 TRP 0.011 0.001 TRP K 455 HIS 0.010 0.001 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00307 (19314) covalent geometry : angle 0.64507 (27302) hydrogen bonds : bond 0.04423 ( 926) hydrogen bonds : angle 4.06157 ( 2343) metal coordination : bond 0.00427 ( 4) metal coordination : angle 1.94289 ( 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 163 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.672 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: 0.7447 (OUTLIER) cc_final: 0.6448 (mp10) REVERT: C 24 GLN cc_start: 0.5496 (OUTLIER) cc_final: 0.5260 (mp10) REVERT: C 64 GLU cc_start: 0.1618 (OUTLIER) cc_final: 0.1359 (pt0) REVERT: C 116 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8585 (pp) REVERT: D 62 MET cc_start: 0.5706 (pmm) cc_final: 0.5329 (mmm) REVERT: D 120 LYS cc_start: 0.7037 (ptpp) cc_final: 0.6695 (ptmm) REVERT: E 65 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7695 (mt) REVERT: G 63 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8739 (mm) REVERT: G 96 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8486 (tp) REVERT: L 278 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: M 20 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8266 (mptt) REVERT: M 32 LYS cc_start: 0.9327 (mmtm) cc_final: 0.9037 (mmmm) REVERT: M 80 LYS cc_start: 0.8980 (pttp) cc_final: 0.8744 (pttm) REVERT: M 83 TYR cc_start: 0.7601 (m-80) cc_final: 0.7296 (m-80) REVERT: M 110 LEU cc_start: 0.9222 (mm) cc_final: 0.8998 (tp) REVERT: N 6 MET cc_start: 0.6654 (tmm) cc_final: 0.6055 (tpp) REVERT: N 25 PHE cc_start: 0.7601 (m-80) cc_final: 0.7051 (m-80) REVERT: N 35 LEU cc_start: 0.7979 (tp) cc_final: 0.7713 (tt) outliers start: 40 outliers final: 19 residues processed: 160 average time/residue: 0.1590 time to fit residues: 38.3388 Evaluate side-chains 131 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE 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 96 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 386 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 148 GLN Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 278 GLN Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain N residue 4 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 59 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 145 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS E 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 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 = 0.4060 r_free = 0.4060 target = 0.080501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.067347 restraints weight = 127138.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.067133 restraints weight = 104956.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.067202 restraints weight = 88650.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.067268 restraints weight = 82944.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.067233 restraints weight = 80775.431| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19318 Z= 0.153 Angle : 0.646 9.902 27305 Z= 0.356 Chirality : 0.039 0.219 3058 Planarity : 0.004 0.060 2471 Dihedral : 27.767 172.979 4896 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 2.69 % Allowed : 19.48 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.21), residues: 1536 helix: 0.20 (0.20), residues: 737 sheet: -0.49 (0.41), residues: 142 loop : -1.08 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.027 0.002 TYR M 76 PHE 0.017 0.001 PHE M 109 TRP 0.011 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00329 (19314) covalent geometry : angle 0.64611 (27302) hydrogen bonds : bond 0.04685 ( 926) hydrogen bonds : angle 4.06772 ( 2343) metal coordination : bond 0.00332 ( 4) metal coordination : angle 1.82956 ( 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 140 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.610 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: 0.7430 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: C 24 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.5272 (mp10) REVERT: C 64 GLU cc_start: 0.1796 (OUTLIER) cc_final: 0.1353 (pt0) REVERT: C 116 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8600 (pp) REVERT: D 62 MET cc_start: 0.5834 (pmm) cc_final: 0.5429 (mmm) REVERT: D 79 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7079 (mtp-110) REVERT: E 65 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (mt) REVERT: E 79 LYS cc_start: 0.7457 (ttmt) cc_final: 0.7139 (ttmt) REVERT: G 63 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8800 (mm) REVERT: G 96 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8448 (tp) REVERT: K 255 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7149 (mmm-85) REVERT: M 32 LYS cc_start: 0.9242 (mmtm) cc_final: 0.8970 (mmmm) REVERT: M 80 LYS cc_start: 0.8970 (pttp) cc_final: 0.8683 (pttm) REVERT: M 83 TYR cc_start: 0.7446 (m-80) cc_final: 0.7146 (m-80) REVERT: N 25 PHE cc_start: 0.7397 (m-80) cc_final: 0.6814 (m-80) REVERT: N 35 LEU cc_start: 0.7988 (tp) cc_final: 0.7743 (tt) outliers start: 36 outliers final: 21 residues processed: 137 average time/residue: 0.1486 time to fit residues: 31.2504 Evaluate side-chains 126 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 96 LEU 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 85 ASP 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 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 386 ILE 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 288 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 176 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 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 = 0.4060 r_free = 0.4060 target = 0.080497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.067444 restraints weight = 127533.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.067243 restraints weight = 108207.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.067287 restraints weight = 90314.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.067384 restraints weight = 85197.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.067323 restraints weight = 82743.009| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19318 Z= 0.149 Angle : 0.643 15.349 27305 Z= 0.351 Chirality : 0.038 0.222 3058 Planarity : 0.004 0.038 2471 Dihedral : 27.729 171.511 4894 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.62 % Favored : 95.18 % Rotamer: Outliers : 3.51 % Allowed : 19.10 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.21), residues: 1536 helix: 0.31 (0.20), residues: 738 sheet: -0.12 (0.42), residues: 135 loop : -1.08 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 33 TYR 0.021 0.002 TYR M 76 PHE 0.011 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 covalent geometry : bond 0.00319 (19314) covalent geometry : angle 0.64236 (27302) hydrogen bonds : bond 0.04536 ( 926) hydrogen bonds : angle 3.99916 ( 2343) metal coordination : bond 0.00401 ( 4) metal coordination : angle 1.70012 ( 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 158 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.609 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: C 24 GLN cc_start: 0.5595 (OUTLIER) cc_final: 0.5345 (mp10) REVERT: C 64 GLU cc_start: 0.1999 (OUTLIER) cc_final: 0.1505 (pt0) REVERT: C 116 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8632 (pp) REVERT: D 62 MET cc_start: 0.5845 (pmm) cc_final: 0.5470 (mmm) REVERT: D 83 TYR cc_start: 0.4686 (m-10) cc_final: 0.3616 (t80) REVERT: D 120 LYS cc_start: 0.7277 (ptpp) cc_final: 0.7002 (ptmm) REVERT: E 65 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7843 (mt) REVERT: G 63 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8780 (mm) REVERT: L 165 MET cc_start: 0.7163 (mpp) cc_final: 0.5154 (mpp) REVERT: M 27 HIS cc_start: 0.6291 (m90) cc_final: 0.6078 (m-70) REVERT: M 72 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8475 (mmmt) REVERT: M 83 TYR cc_start: 0.7492 (m-80) cc_final: 0.7147 (m-80) REVERT: M 110 LEU cc_start: 0.9289 (tp) cc_final: 0.9086 (mm) REVERT: N 25 PHE cc_start: 0.7425 (m-80) cc_final: 0.6764 (m-80) REVERT: N 46 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7794 (pttt) outliers start: 47 outliers final: 28 residues processed: 155 average time/residue: 0.1575 time to fit residues: 36.9331 Evaluate side-chains 138 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE 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 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 97 LEU 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 255 ARG Chi-restraints excluded: chain K residue 386 ILE 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 L residue 288 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 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 = 0.4037 r_free = 0.4037 target = 0.079540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.065802 restraints weight = 126514.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065726 restraints weight = 101425.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.065791 restraints weight = 82141.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.065869 restraints weight = 76539.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065848 restraints weight = 71875.216| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4601 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= 0.187 Angle : 0.684 15.887 27305 Z= 0.373 Chirality : 0.040 0.217 3058 Planarity : 0.004 0.041 2471 Dihedral : 27.857 169.978 4892 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.60 % Favored : 94.21 % Rotamer: Outliers : 3.96 % Allowed : 19.40 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.21), residues: 1536 helix: 0.11 (0.19), residues: 736 sheet: -0.04 (0.42), residues: 133 loop : -1.19 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 33 TYR 0.019 0.002 TYR M 76 PHE 0.014 0.001 PHE H 70 TRP 0.014 0.001 TRP L 193 HIS 0.010 0.002 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00413 (19314) covalent geometry : angle 0.68357 (27302) hydrogen bonds : bond 0.05488 ( 926) hydrogen bonds : angle 4.20996 ( 2343) metal coordination : bond 0.00366 ( 4) metal coordination : angle 1.63219 ( 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 159 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 0.714 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: C 24 GLN cc_start: 0.5495 (OUTLIER) cc_final: 0.5183 (mp10) REVERT: C 96 LEU cc_start: 0.3678 (OUTLIER) cc_final: 0.3320 (mp) REVERT: C 116 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8601 (pp) REVERT: D 62 MET cc_start: 0.6515 (pmm) cc_final: 0.5822 (mmm) REVERT: D 83 TYR cc_start: 0.5612 (m-10) cc_final: 0.4629 (t80) REVERT: D 120 LYS cc_start: 0.7289 (ptpp) cc_final: 0.7049 (ptmm) REVERT: E 65 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7880 (mt) REVERT: M 27 HIS cc_start: 0.6466 (m90) cc_final: 0.6191 (m-70) REVERT: M 72 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8546 (mmmt) REVERT: M 83 TYR cc_start: 0.7647 (m-80) cc_final: 0.7185 (m-80) REVERT: N 25 PHE cc_start: 0.7577 (m-80) cc_final: 0.6814 (m-80) REVERT: N 35 LEU cc_start: 0.7920 (tp) cc_final: 0.7676 (tt) REVERT: N 46 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7934 (pttm) outliers start: 53 outliers final: 35 residues processed: 152 average time/residue: 0.1528 time to fit residues: 35.2669 Evaluate side-chains 142 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN 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 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 63 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 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 255 ARG Chi-restraints excluded: chain K residue 386 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 76 TYR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 64 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 172 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.080598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067730 restraints weight = 126481.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067563 restraints weight = 117222.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.067687 restraints weight = 90304.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.067719 restraints weight = 85991.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.067702 restraints weight = 83047.246| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19318 Z= 0.144 Angle : 0.653 16.300 27305 Z= 0.352 Chirality : 0.038 0.210 3058 Planarity : 0.004 0.044 2471 Dihedral : 27.675 169.963 4892 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.56 % Favored : 95.25 % Rotamer: Outliers : 2.76 % Allowed : 20.67 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1536 helix: 0.33 (0.20), residues: 731 sheet: 0.13 (0.43), residues: 133 loop : -1.18 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 33 TYR 0.020 0.001 TYR M 76 PHE 0.023 0.001 PHE M 109 TRP 0.009 0.001 TRP L 193 HIS 0.009 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (19314) covalent geometry : angle 0.65309 (27302) hydrogen bonds : bond 0.04371 ( 926) hydrogen bonds : angle 4.03345 ( 2343) metal coordination : bond 0.00600 ( 4) metal coordination : angle 1.60593 ( 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 150 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.598 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: B 88 TYR cc_start: 0.6077 (m-10) cc_final: 0.5641 (m-80) REVERT: C 64 GLU cc_start: 0.2186 (OUTLIER) cc_final: 0.1701 (pt0) REVERT: C 96 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.3369 (mp) REVERT: C 116 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (pp) REVERT: D 59 MET cc_start: 0.6102 (tpp) cc_final: 0.5535 (tpp) REVERT: D 83 TYR cc_start: 0.5590 (m-10) cc_final: 0.4350 (t80) REVERT: E 65 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7749 (mt) REVERT: G 63 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8786 (mm) REVERT: K 255 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7083 (mmm-85) REVERT: L 265 MET cc_start: 0.6361 (tpp) cc_final: 0.6151 (tpt) REVERT: M 27 HIS cc_start: 0.6088 (m90) cc_final: 0.5867 (m-70) REVERT: M 72 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8341 (mmmt) REVERT: M 83 TYR cc_start: 0.7378 (m-80) cc_final: 0.6988 (m-10) REVERT: N 2 ASP cc_start: 0.6969 (m-30) cc_final: 0.6468 (t0) REVERT: N 6 MET cc_start: 0.6538 (tmm) cc_final: 0.6016 (tpp) REVERT: N 25 PHE cc_start: 0.7310 (m-80) cc_final: 0.6655 (m-80) REVERT: N 46 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7887 (pttt) outliers start: 37 outliers final: 25 residues processed: 146 average time/residue: 0.1530 time to fit residues: 33.7352 Evaluate side-chains 137 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 64 GLU 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 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 43 VAL 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 63 LEU Chi-restraints excluded: chain G residue 96 LEU 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 255 ARG Chi-restraints excluded: chain K residue 386 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 143 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 144 optimal weight: 0.5980 chunk 178 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.080728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.067718 restraints weight = 127247.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.067379 restraints weight = 95169.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.067299 restraints weight = 89616.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.067324 restraints weight = 80499.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.067362 restraints weight = 75993.900| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19318 Z= 0.147 Angle : 0.670 14.997 27305 Z= 0.360 Chirality : 0.038 0.197 3058 Planarity : 0.004 0.044 2471 Dihedral : 27.656 168.131 4889 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.82 % Favored : 94.99 % Rotamer: Outliers : 2.91 % Allowed : 20.45 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.21), residues: 1536 helix: 0.34 (0.20), residues: 736 sheet: 0.11 (0.43), residues: 135 loop : -1.15 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 33 TYR 0.022 0.001 TYR M 76 PHE 0.052 0.001 PHE M 109 TRP 0.008 0.001 TRP L 193 HIS 0.019 0.001 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00312 (19314) covalent geometry : angle 0.66935 (27302) hydrogen bonds : bond 0.04514 ( 926) hydrogen bonds : angle 4.06603 ( 2343) metal coordination : bond 0.00506 ( 4) metal coordination : angle 1.66297 ( 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 149 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.594 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: 0.7019 (mmm) cc_final: 0.6444 (mmm) REVERT: B 88 TYR cc_start: 0.6152 (m-10) cc_final: 0.5671 (m-80) REVERT: C 116 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8659 (pp) REVERT: E 65 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7648 (mt) REVERT: G 63 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8802 (mm) REVERT: K 255 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6832 (mmm-85) REVERT: M 27 HIS cc_start: 0.6354 (m90) cc_final: 0.6066 (m-70) REVERT: M 52 PHE cc_start: 0.7995 (m-80) cc_final: 0.7701 (m-80) REVERT: M 72 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8473 (mmmt) REVERT: M 83 TYR cc_start: 0.7594 (m-80) cc_final: 0.7096 (m-10) REVERT: N 2 ASP cc_start: 0.7119 (m-30) cc_final: 0.6616 (t0) REVERT: N 6 MET cc_start: 0.6478 (tmm) cc_final: 0.5990 (tpp) REVERT: N 25 PHE cc_start: 0.7375 (m-80) cc_final: 0.6798 (m-80) REVERT: N 46 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7963 (pttt) outliers start: 39 outliers final: 29 residues processed: 146 average time/residue: 0.1513 time to fit residues: 33.3501 Evaluate side-chains 139 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 100 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 43 VAL 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 63 LEU Chi-restraints excluded: chain G residue 96 LEU 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 255 ARG Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 386 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 284 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 105 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 0.0870 chunk 143 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.080057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.066861 restraints weight = 127002.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.066697 restraints weight = 101128.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.066637 restraints weight = 88939.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.066732 restraints weight = 80002.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.066745 restraints weight = 75800.477| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19318 Z= 0.171 Angle : 0.689 14.046 27305 Z= 0.372 Chirality : 0.039 0.210 3058 Planarity : 0.004 0.044 2471 Dihedral : 27.737 167.300 4889 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 2.91 % Allowed : 20.52 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.21), residues: 1536 helix: 0.19 (0.20), residues: 735 sheet: 0.11 (0.43), residues: 135 loop : -1.17 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.038 0.002 TYR D 83 PHE 0.050 0.002 PHE M 109 TRP 0.010 0.001 TRP L 193 HIS 0.024 0.002 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00374 (19314) covalent geometry : angle 0.68927 (27302) hydrogen bonds : bond 0.05106 ( 926) hydrogen bonds : angle 4.17756 ( 2343) metal coordination : bond 0.00420 ( 4) metal coordination : angle 1.70545 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.72 seconds wall clock time: 56 minutes 35.18 seconds (3395.18 seconds total)