Starting phenix.real_space_refine on Mon May 19 06:48:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol1_16936/05_2025/8ol1_16936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol1_16936/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ol1_16936/05_2025/8ol1_16936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol1_16936/05_2025/8ol1_16936.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol1_16936/05_2025/8ol1_16936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol1_16936/05_2025/8ol1_16936.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.68, per 1000 atoms: 0.58 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: 4.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 8.01 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: 8.73 Time building geometry restraints manager: 5.02 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.370 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.059 0.015 TRP K 455 HIS 0.022 0.004 HIS L 310 PHE 0.071 0.013 PHE L 150 TYR 0.200 0.029 TYR C 57 ARG 0.021 0.002 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.19480 ( 926) hydrogen bonds : angle 7.85497 ( 2343) metal coordination : bond 0.15921 ( 4) metal coordination : angle 8.22331 ( 3) covalent geometry : bond 0.01332 (19314) covalent geometry : angle 2.02289 (27302) *********************** 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 : 1.635 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: 0.3713 time to fit residues: 129.0187 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 : 1.584 ------------------------------------------------------------------------------- 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 151 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 162 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.080207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.067981 restraints weight = 128052.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067639 restraints weight = 113209.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.067607 restraints weight = 102033.975| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19318 Z= 0.189 Angle : 0.779 11.986 27305 Z= 0.438 Chirality : 0.045 0.254 3058 Planarity : 0.005 0.038 2471 Dihedral : 28.570 178.902 4942 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.69 % Favored : 94.99 % Rotamer: Outliers : 3.43 % Allowed : 14.78 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1536 helix: -0.79 (0.19), residues: 735 sheet: -0.59 (0.42), residues: 133 loop : -1.20 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 193 HIS 0.025 0.002 HIS L 283 PHE 0.014 0.002 PHE N 93 TYR 0.025 0.002 TYR L 279 ARG 0.005 0.001 ARG K 246 Details of bonding type rmsd hydrogen bonds : bond 0.06446 ( 926) hydrogen bonds : angle 4.77630 ( 2343) metal coordination : bond 0.00920 ( 4) metal coordination : angle 2.55481 ( 3) covalent geometry : bond 0.00397 (19314) covalent geometry : angle 0.77837 (27302) *********************** 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 186 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.708 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 63 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: B 93 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6479 (mp10) REVERT: C 24 GLN cc_start: 0.5912 (OUTLIER) cc_final: 0.5637 (mp10) REVERT: D 62 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5807 (mmm) REVERT: D 68 ASP cc_start: 0.5972 (t0) cc_final: 0.5765 (t0) REVERT: D 79 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7146 (mtp-110) REVERT: D 83 TYR cc_start: 0.3191 (m-10) cc_final: 0.2830 (t80) REVERT: G 63 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.8795 (mm) REVERT: L 278 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.6036 (pp30) REVERT: M 27 HIS cc_start: 0.7056 (m170) cc_final: 0.6820 (m90) REVERT: M 30 ILE cc_start: 0.3270 (OUTLIER) cc_final: 0.3024 (tp) REVERT: M 38 THR cc_start: 0.8431 (m) cc_final: 0.8213 (p) REVERT: N 2 ASP cc_start: 0.7345 (m-30) cc_final: 0.7053 (m-30) REVERT: N 6 MET cc_start: 0.6051 (tmm) cc_final: 0.5272 (tpp) REVERT: N 25 PHE cc_start: 0.7186 (m-80) cc_final: 0.6671 (m-10) REVERT: N 99 LEU cc_start: 0.7758 (mp) cc_final: 0.7248 (mt) outliers start: 46 outliers final: 17 residues processed: 182 average time/residue: 0.3422 time to fit residues: 90.8366 Evaluate side-chains 138 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 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 278 GLN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain N residue 68 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN ** L 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.079645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.066262 restraints weight = 127262.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.066249 restraints weight = 106562.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.066209 restraints weight = 86948.229| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3478 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= 0.180 Angle : 0.713 11.389 27305 Z= 0.398 Chirality : 0.042 0.222 3058 Planarity : 0.005 0.044 2471 Dihedral : 28.143 177.947 4917 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.01 % Favored : 94.86 % Rotamer: Outliers : 3.66 % Allowed : 16.12 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1536 helix: -0.39 (0.19), residues: 729 sheet: -0.53 (0.42), residues: 129 loop : -1.19 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 193 HIS 0.018 0.002 HIS L 283 PHE 0.014 0.002 PHE H 70 TYR 0.023 0.002 TYR L 279 ARG 0.006 0.001 ARG N 37 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 926) hydrogen bonds : angle 4.45269 ( 2343) metal coordination : bond 0.00384 ( 4) metal coordination : angle 1.83306 ( 3) covalent geometry : bond 0.00388 (19314) covalent geometry : angle 0.71252 (27302) *********************** 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 171 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.620 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 93 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: C 24 GLN cc_start: 0.5783 (OUTLIER) cc_final: 0.5461 (mp10) REVERT: D 62 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5640 (mmm) REVERT: D 79 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7222 (mtp180) REVERT: M 27 HIS cc_start: 0.7807 (m170) cc_final: 0.7494 (m90) REVERT: M 30 ILE cc_start: 0.3310 (OUTLIER) cc_final: 0.3049 (tp) REVERT: M 110 LEU cc_start: 0.9252 (mm) cc_final: 0.9037 (tp) REVERT: N 6 MET cc_start: 0.6522 (tmm) cc_final: 0.5707 (tpp) REVERT: N 25 PHE cc_start: 0.7349 (m-80) cc_final: 0.6736 (m-80) outliers start: 49 outliers final: 28 residues processed: 165 average time/residue: 0.3073 time to fit residues: 76.8325 Evaluate side-chains 142 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 62 ILE 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 D residue 66 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 97 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 L residue 144 LEU Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL 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 40 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 2 optimal weight: 0.0370 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 overall best weight: 1.7862 ------------------------------------------------------------------------------- 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** C 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.079803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.066055 restraints weight = 127207.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.066050 restraints weight = 102076.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.066099 restraints weight = 82154.632| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19318 Z= 0.172 Angle : 0.683 13.500 27305 Z= 0.380 Chirality : 0.041 0.265 3058 Planarity : 0.004 0.042 2471 Dihedral : 28.016 176.540 4911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.01 % Favored : 94.86 % Rotamer: Outliers : 3.96 % Allowed : 17.39 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1536 helix: -0.20 (0.19), residues: 732 sheet: -0.48 (0.41), residues: 132 loop : -1.21 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 193 HIS 0.016 0.002 HIS L 283 PHE 0.015 0.001 PHE M 109 TYR 0.026 0.002 TYR M 79 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 926) hydrogen bonds : angle 4.33198 ( 2343) metal coordination : bond 0.00358 ( 4) metal coordination : angle 1.92482 ( 3) covalent geometry : bond 0.00375 (19314) covalent geometry : angle 0.68244 (27302) *********************** 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 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: C 24 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5310 (mp10) REVERT: C 116 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8475 (pp) REVERT: D 59 MET cc_start: 0.6097 (tpp) cc_final: 0.5331 (tpp) REVERT: D 62 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5602 (mmm) REVERT: D 79 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7143 (mtp180) REVERT: D 100 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6356 (pt) REVERT: E 79 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7339 (mttp) REVERT: E 93 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: M 30 ILE cc_start: 0.3421 (OUTLIER) cc_final: 0.3141 (tp) REVERT: M 83 TYR cc_start: 0.7565 (m-80) cc_final: 0.7304 (m-80) REVERT: N 6 MET cc_start: 0.6323 (tmm) cc_final: 0.5741 (tpp) REVERT: N 25 PHE cc_start: 0.7490 (m-80) cc_final: 0.6810 (m-80) REVERT: N 35 LEU cc_start: 0.7803 (tp) cc_final: 0.7582 (tt) outliers start: 53 outliers final: 29 residues processed: 166 average time/residue: 0.3181 time to fit residues: 79.0131 Evaluate side-chains 139 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 93 GLN 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 K residue 255 ARG Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 223 HIS Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 4 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 77 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 278 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 = 0.4022 r_free = 0.4022 target = 0.078918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.065390 restraints weight = 127897.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.065163 restraints weight = 102868.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.065025 restraints weight = 91651.795| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19318 Z= 0.209 Angle : 0.713 10.588 27305 Z= 0.393 Chirality : 0.042 0.245 3058 Planarity : 0.005 0.048 2471 Dihedral : 28.061 173.358 4907 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 5.22 % Allowed : 17.16 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1536 helix: -0.35 (0.19), residues: 731 sheet: -0.61 (0.41), residues: 123 loop : -1.25 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 193 HIS 0.014 0.002 HIS L 283 PHE 0.016 0.002 PHE H 70 TYR 0.024 0.002 TYR M 76 ARG 0.006 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06027 ( 926) hydrogen bonds : angle 4.47907 ( 2343) metal coordination : bond 0.00445 ( 4) metal coordination : angle 1.83003 ( 3) covalent geometry : bond 0.00464 (19314) covalent geometry : angle 0.71313 (27302) *********************** 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 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 109 time to evaluate : 1.599 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 93 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6754 (mp10) REVERT: C 24 GLN cc_start: 0.5459 (OUTLIER) cc_final: 0.5047 (mp10) REVERT: C 116 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8573 (pp) REVERT: D 62 MET cc_start: 0.6670 (pmm) cc_final: 0.6029 (mmt) REVERT: D 79 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7106 (mtp180) REVERT: D 120 LYS cc_start: 0.7291 (ptpp) cc_final: 0.6950 (ptmm) REVERT: E 56 LYS cc_start: 0.7362 (mmmm) cc_final: 0.7137 (ttmm) REVERT: E 65 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8028 (mt) REVERT: E 81 ASP cc_start: 0.6824 (t0) cc_final: 0.6597 (t0) REVERT: E 93 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: M 27 HIS cc_start: 0.6256 (m90) cc_final: 0.6038 (m90) REVERT: M 30 ILE cc_start: 0.3546 (OUTLIER) cc_final: 0.3165 (tp) REVERT: M 82 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7059 (ptt180) REVERT: M 110 LEU cc_start: 0.9184 (mm) cc_final: 0.8957 (tp) REVERT: N 6 MET cc_start: 0.6515 (tmm) cc_final: 0.5864 (tpp) REVERT: N 25 PHE cc_start: 0.7624 (m-80) cc_final: 0.7000 (m-80) REVERT: N 35 LEU cc_start: 0.8010 (tp) cc_final: 0.7750 (tt) outliers start: 70 outliers final: 46 residues processed: 175 average time/residue: 0.2796 time to fit residues: 75.4110 Evaluate side-chains 151 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 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 180 HIS Chi-restraints excluded: chain L residue 267 VAL 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 30 ILE Chi-restraints excluded: chain M residue 31 VAL 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 44 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 158 optimal weight: 0.0050 chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 169 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.080299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.066281 restraints weight = 128165.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.066252 restraints weight = 93594.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.066480 restraints weight = 80565.034| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19318 Z= 0.146 Angle : 0.649 9.939 27305 Z= 0.357 Chirality : 0.039 0.220 3058 Planarity : 0.004 0.046 2471 Dihedral : 27.826 173.599 4902 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.01 % Favored : 94.86 % Rotamer: Outliers : 3.21 % Allowed : 20.00 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1536 helix: 0.06 (0.19), residues: 734 sheet: -0.36 (0.42), residues: 125 loop : -1.24 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 193 HIS 0.012 0.001 HIS L 283 PHE 0.017 0.001 PHE M 109 TYR 0.039 0.002 TYR M 76 ARG 0.007 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 926) hydrogen bonds : angle 4.16409 ( 2343) metal coordination : bond 0.00577 ( 4) metal coordination : angle 1.75535 ( 3) covalent geometry : bond 0.00307 (19314) covalent geometry : angle 0.64880 (27302) *********************** 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 160 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 1.682 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 93 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6347 (mp10) REVERT: C 24 GLN cc_start: 0.5522 (OUTLIER) cc_final: 0.5244 (mp10) REVERT: C 64 GLU cc_start: 0.1718 (OUTLIER) cc_final: 0.1446 (pt0) REVERT: C 116 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8551 (pp) REVERT: D 62 MET cc_start: 0.6200 (pmm) cc_final: 0.5558 (mmm) REVERT: D 79 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7139 (mtp-110) REVERT: D 120 LYS cc_start: 0.7253 (ptpp) cc_final: 0.6927 (ptmm) REVERT: E 65 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7899 (mt) REVERT: E 93 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: F 63 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6964 (mm-30) REVERT: G 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8743 (mm) REVERT: G 96 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8494 (tp) REVERT: L 265 MET cc_start: 0.7539 (tpp) cc_final: 0.7242 (tpp) REVERT: M 20 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8079 (mptt) REVERT: M 27 HIS cc_start: 0.6687 (m90) cc_final: 0.6364 (m-70) REVERT: M 72 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8698 (mmmt) REVERT: M 110 LEU cc_start: 0.9308 (mm) cc_final: 0.9002 (tp) REVERT: N 6 MET cc_start: 0.6494 (tmm) cc_final: 0.5958 (tpp) REVERT: N 25 PHE cc_start: 0.7808 (m-80) cc_final: 0.7077 (m-80) REVERT: N 35 LEU cc_start: 0.8054 (tp) cc_final: 0.7818 (tt) REVERT: N 46 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7624 (pttm) outliers start: 43 outliers final: 26 residues processed: 158 average time/residue: 0.3338 time to fit residues: 78.1869 Evaluate side-chains 140 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 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 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 31 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 46 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** 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 = 0.4025 r_free = 0.4025 target = 0.079051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065572 restraints weight = 126180.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.065611 restraints weight = 101902.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065523 restraints weight = 85031.232| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19318 Z= 0.205 Angle : 0.708 15.939 27305 Z= 0.387 Chirality : 0.041 0.229 3058 Planarity : 0.005 0.050 2471 Dihedral : 27.987 171.263 4902 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.95 % Rotamer: Outliers : 3.88 % Allowed : 19.85 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1536 helix: -0.11 (0.19), residues: 737 sheet: -0.35 (0.42), residues: 122 loop : -1.29 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 193 HIS 0.010 0.002 HIS L 283 PHE 0.016 0.002 PHE H 70 TYR 0.034 0.002 TYR M 76 ARG 0.003 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.05844 ( 926) hydrogen bonds : angle 4.39911 ( 2343) metal coordination : bond 0.00392 ( 4) metal coordination : angle 1.85192 ( 3) covalent geometry : bond 0.00457 (19314) covalent geometry : angle 0.70752 (27302) *********************** 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 159 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.839 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 93 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: C 24 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4990 (mp10) REVERT: C 116 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8593 (pp) REVERT: D 62 MET cc_start: 0.6402 (pmm) cc_final: 0.5688 (mmt) REVERT: D 79 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7123 (mtp180) REVERT: D 120 LYS cc_start: 0.7416 (ptpp) cc_final: 0.7137 (ptmm) REVERT: E 65 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7899 (mt) REVERT: E 93 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: M 72 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8498 (mmmt) REVERT: N 25 PHE cc_start: 0.7506 (m-80) cc_final: 0.6869 (m-80) REVERT: N 46 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7759 (pttm) outliers start: 52 outliers final: 36 residues processed: 154 average time/residue: 0.3217 time to fit residues: 73.9054 Evaluate side-chains 138 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain 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 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain 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 219 ILE 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 31 VAL Chi-restraints excluded: chain N residue 4 PHE Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 HIS ** 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 = 0.4026 r_free = 0.4026 target = 0.079074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.065749 restraints weight = 125924.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065637 restraints weight = 110690.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.065747 restraints weight = 84682.420| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19318 Z= 0.187 Angle : 0.701 15.126 27305 Z= 0.380 Chirality : 0.040 0.228 3058 Planarity : 0.004 0.046 2471 Dihedral : 27.958 171.486 4902 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.92 % Favored : 93.88 % Rotamer: Outliers : 3.81 % Allowed : 19.93 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1536 helix: -0.14 (0.19), residues: 736 sheet: -0.24 (0.44), residues: 122 loop : -1.35 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 193 HIS 0.010 0.001 HIS L 283 PHE 0.019 0.001 PHE M 109 TYR 0.025 0.002 TYR C 39 ARG 0.003 0.000 ARG M 82 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 926) hydrogen bonds : angle 4.37675 ( 2343) metal coordination : bond 0.00461 ( 4) metal coordination : angle 1.65324 ( 3) covalent geometry : bond 0.00417 (19314) covalent geometry : angle 0.70072 (27302) *********************** 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 158 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 1.647 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: 0.7479 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: C 24 GLN cc_start: 0.5413 (OUTLIER) cc_final: 0.4988 (mp10) REVERT: C 73 ASN cc_start: 0.7943 (t0) cc_final: 0.7719 (t0) REVERT: C 116 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8573 (pp) REVERT: D 79 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7324 (mtp-110) REVERT: D 83 TYR cc_start: 0.4951 (m-10) cc_final: 0.3588 (t80) REVERT: D 120 LYS cc_start: 0.7522 (ptpp) cc_final: 0.7297 (ptmm) REVERT: E 65 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7931 (mt) REVERT: E 93 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: L 319 MET cc_start: 0.2004 (tmm) cc_final: 0.1367 (tmm) REVERT: M 1 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8000 (ppp) REVERT: M 72 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8574 (mmmt) REVERT: N 25 PHE cc_start: 0.7303 (m-80) cc_final: 0.6727 (m-80) REVERT: N 35 LEU cc_start: 0.7646 (tp) cc_final: 0.7406 (tt) REVERT: N 46 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7834 (pttm) outliers start: 51 outliers final: 39 residues processed: 154 average time/residue: 0.2924 time to fit residues: 68.6426 Evaluate side-chains 148 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR 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 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 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 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 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 219 ILE 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 L residue 317 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 4 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 119 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.9464 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.079339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.066232 restraints weight = 126503.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066126 restraints weight = 112493.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.066206 restraints weight = 89033.955| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19318 Z= 0.171 Angle : 0.679 15.211 27305 Z= 0.370 Chirality : 0.039 0.223 3058 Planarity : 0.004 0.044 2471 Dihedral : 27.898 170.251 4902 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.79 % Favored : 94.01 % Rotamer: Outliers : 3.73 % Allowed : 20.15 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1536 helix: -0.04 (0.19), residues: 736 sheet: -0.08 (0.43), residues: 123 loop : -1.33 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 PHE 0.015 0.001 PHE N 93 TYR 0.023 0.002 TYR C 39 ARG 0.002 0.000 ARG L 262 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 926) hydrogen bonds : angle 4.27466 ( 2343) metal coordination : bond 0.00537 ( 4) metal coordination : angle 1.68313 ( 3) covalent geometry : bond 0.00376 (19314) covalent geometry : angle 0.67845 (27302) *********************** 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 157 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 1.774 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 93 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: C 24 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.5124 (mp10) REVERT: C 116 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8545 (pp) REVERT: D 62 MET cc_start: 0.6357 (pmm) cc_final: 0.5793 (mmt) REVERT: D 83 TYR cc_start: 0.4565 (m-10) cc_final: 0.3489 (t80) REVERT: D 120 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7663 (ptmm) REVERT: E 65 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (mt) REVERT: E 79 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7378 (mtmt) REVERT: E 93 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: L 319 MET cc_start: 0.2263 (tmm) cc_final: 0.1671 (tmm) REVERT: M 72 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8527 (mmmt) REVERT: N 6 MET cc_start: 0.6410 (tmm) cc_final: 0.5917 (tpp) REVERT: N 25 PHE cc_start: 0.7246 (m-80) cc_final: 0.6670 (m-80) REVERT: N 46 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7846 (pttm) outliers start: 50 outliers final: 35 residues processed: 152 average time/residue: 0.3120 time to fit residues: 72.0292 Evaluate side-chains 146 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR 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 93 GLN 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 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 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 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 L residue 317 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 31 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 36 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 120 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.079613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.066349 restraints weight = 126325.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.066197 restraints weight = 114569.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.066337 restraints weight = 88138.627| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4928 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= 0.159 Angle : 0.668 16.608 27305 Z= 0.363 Chirality : 0.039 0.218 3058 Planarity : 0.004 0.044 2471 Dihedral : 27.843 169.551 4894 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 3.28 % Allowed : 20.52 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1536 helix: 0.06 (0.20), residues: 737 sheet: 0.08 (0.44), residues: 123 loop : -1.31 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 PHE 0.016 0.001 PHE N 93 TYR 0.021 0.002 TYR C 39 ARG 0.006 0.000 ARG K 255 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 926) hydrogen bonds : angle 4.23743 ( 2343) metal coordination : bond 0.00571 ( 4) metal coordination : angle 1.69485 ( 3) covalent geometry : bond 0.00345 (19314) covalent geometry : angle 0.66804 (27302) ********************** 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 152 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.609 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: C 24 GLN cc_start: 0.5560 (OUTLIER) cc_final: 0.5092 (mp10) REVERT: C 116 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8545 (pp) REVERT: D 62 MET cc_start: 0.6338 (pmm) cc_final: 0.5777 (mmt) REVERT: D 83 TYR cc_start: 0.5474 (m-10) cc_final: 0.4111 (t80) REVERT: D 120 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7830 (ptmm) REVERT: E 65 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7856 (mt) REVERT: E 79 LYS cc_start: 0.7613 (ttmt) cc_final: 0.7369 (mtmt) REVERT: E 93 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: L 319 MET cc_start: 0.2231 (tmm) cc_final: 0.1661 (tmm) REVERT: M 72 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8481 (mmmt) REVERT: N 6 MET cc_start: 0.6370 (tmm) cc_final: 0.5889 (tpp) REVERT: N 25 PHE cc_start: 0.7306 (m-80) cc_final: 0.6749 (m-80) REVERT: N 46 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7857 (pttm) outliers start: 44 outliers final: 36 residues processed: 148 average time/residue: 0.2927 time to fit residues: 66.4273 Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 33 LEU 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 101 THR 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 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 26 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 G residue 97 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 239 LEU 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 L residue 299 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain M residue 1 MET 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 163 optimal weight: 40.0000 chunk 58 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.079699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.066221 restraints weight = 125538.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065897 restraints weight = 95841.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065711 restraints weight = 94461.254| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19318 Z= 0.156 Angle : 0.664 16.641 27305 Z= 0.362 Chirality : 0.039 0.216 3058 Planarity : 0.004 0.066 2471 Dihedral : 27.785 168.480 4893 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 3.21 % Allowed : 20.90 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1536 helix: 0.12 (0.20), residues: 734 sheet: 0.23 (0.44), residues: 123 loop : -1.28 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 193 HIS 0.009 0.001 HIS L 283 PHE 0.032 0.001 PHE M 109 TYR 0.019 0.002 TYR M 76 ARG 0.005 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 926) hydrogen bonds : angle 4.18657 ( 2343) metal coordination : bond 0.00536 ( 4) metal coordination : angle 1.65803 ( 3) covalent geometry : bond 0.00339 (19314) covalent geometry : angle 0.66427 (27302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5302.62 seconds wall clock time: 93 minutes 42.81 seconds (5622.81 seconds total)