Starting phenix.real_space_refine on Sat Sep 12 10:55:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mup_9251/09_2026/6mup_9251.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mup_9251/09_2026/6mup_9251.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/6mup_9251/09_2026/6mup_9251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mup_9251/09_2026/6mup_9251.map" model { file = "/net/cci-nas-00/data/ceres_data/6mup_9251/09_2026/6mup_9251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mup_9251/09_2026/6mup_9251.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 24 5.16 5 C 9101 2.51 5 N 2892 2.21 5 O 3494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 814 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 809 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3027 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 174 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 169 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "M" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.19 Number of scatterers: 15803 At special positions: 0 Unit cell: (150.52, 126.14, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 292 15.00 O 3494 8.00 N 2892 7.00 C 9101 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: 0.99 Conformation dependent library (CDL) restraints added in 385.4 milliseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 54.0% alpha, 3.9% beta 63 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.547A pdb=" N ARG A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.812A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.001A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.798A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.248A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.839A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.896A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.658A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 removed outlier: 3.676A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.517A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.677A pdb=" N ALA C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.528A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.518A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.799A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.788A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.671A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 3.595A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.548A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.621A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 114 removed outlier: 4.313A pdb=" N HIS E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 4.387A pdb=" N LEU E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.535A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 3.851A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.828A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.784A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.512A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.865A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 80 through 88 removed outlier: 4.059A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.696A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.928A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 removed outlier: 3.718A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 Processing helix chain 'H' and resid 91 through 102 removed outlier: 3.610A pdb=" N GLN H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.781A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.507A pdb=" N LYS M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 19 No H-bonds generated for 'chain 'M' and resid 17 through 19' Processing helix chain 'M' and resid 20 through 29 removed outlier: 3.504A pdb=" N ILE M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA M 27 " --> pdb=" O THR M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 44 through 60 removed outlier: 3.973A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE M 53 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 55 " --> pdb=" O HIS M 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU M 58 " --> pdb=" O HIS M 54 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG M 60 " --> pdb=" O CYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 removed outlier: 4.604A pdb=" N LEU M 68 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 106 removed outlier: 3.853A pdb=" N ASN M 106 " --> pdb=" O LYS M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 4.291A pdb=" N THR M 180 " --> pdb=" O GLY M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 206 Processing helix chain 'M' and resid 206 through 211 removed outlier: 3.761A pdb=" N GLN M 211 " --> pdb=" O LYS M 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 removed outlier: 3.580A pdb=" N ARG N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 19 removed outlier: 6.241A pdb=" N ASN N 19 " --> pdb=" O ILE N 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 16 through 19' Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.614A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.051A pdb=" N GLN N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU N 58 " --> pdb=" O HIS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 4.567A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 Processing helix chain 'N' and resid 171 through 183 removed outlier: 4.097A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN N 177 " --> pdb=" O PRO N 173 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 206 Processing helix chain 'N' and resid 206 through 211 removed outlier: 3.763A pdb=" N GLN N 211 " --> pdb=" O LYS N 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.353A pdb=" N ASN A 85 " --> 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 'C' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.336A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.833A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'M' and resid 133 through 134 removed outlier: 5.072A pdb=" N TYR M 151 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 161 " --> pdb=" O PHE M 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE M 86 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN M 87 " --> pdb=" O VAL M 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 133 through 134 removed outlier: 5.199A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2736 1.32 - 1.45: 5656 1.45 - 1.57: 7685 1.57 - 1.69: 581 1.69 - 1.82: 44 Bond restraints: 16702 Sorted by residual: bond pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 1.331 1.496 -0.166 1.38e-02 5.25e+03 1.44e+02 bond pdb=" C VAL C 107 " pdb=" N LEU C 108 " ideal model delta sigma weight residual 1.331 1.238 0.093 1.48e-02 4.57e+03 3.95e+01 bond pdb=" C3' DT J 49 " pdb=" O3' DT J 49 " ideal model delta sigma weight residual 1.435 1.363 0.072 1.30e-02 5.92e+03 3.05e+01 bond pdb=" C3' DG J 48 " pdb=" O3' DG J 48 " ideal model delta sigma weight residual 1.435 1.363 0.072 1.30e-02 5.92e+03 3.05e+01 bond pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " ideal model delta sigma weight residual 1.435 1.372 0.063 1.30e-02 5.92e+03 2.38e+01 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 23390 3.55 - 7.10: 395 7.10 - 10.65: 29 10.65 - 14.21: 2 14.21 - 17.76: 3 Bond angle restraints: 23819 Sorted by residual: angle pdb=" CA SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 115.90 133.64 -17.74 1.21e+00 6.83e-01 2.15e+02 angle pdb=" O SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 122.59 104.83 17.76 1.35e+00 5.49e-01 1.73e+02 angle pdb=" C SER M 195 " pdb=" N ARG M 196 " pdb=" CA ARG M 196 " ideal model delta sigma weight residual 122.79 140.27 -17.48 1.78e+00 3.16e-01 9.64e+01 angle pdb=" O4' DA J -48 " pdb=" C1' DA J -48 " pdb=" N9 DA J -48 " ideal model delta sigma weight residual 108.00 113.45 -5.45 7.00e-01 2.04e+00 6.06e+01 angle pdb=" N PRO G 117 " pdb=" CA PRO G 117 " pdb=" CB PRO G 117 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 ... (remaining 23814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7907 35.00 - 70.00: 1387 70.00 - 105.00: 52 105.00 - 140.00: 0 140.00 - 175.01: 2 Dihedral angle restraints: 9348 sinusoidal: 5774 harmonic: 3574 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 111.61 68.39 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA LEU E 135 " pdb=" C LEU E 135 " pdb=" N GLU E 136 " pdb=" CA GLU E 136 " ideal model delta harmonic sigma weight residual 180.00 133.88 46.12 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual 180.00 133.96 46.04 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 9345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2033 0.074 - 0.149: 581 0.149 - 0.223: 63 0.223 - 0.297: 12 0.297 - 0.372: 1 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA SER K 528 " pdb=" N SER K 528 " pdb=" C SER K 528 " pdb=" CB SER K 528 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL D 66 " pdb=" CA VAL D 66 " pdb=" CG1 VAL D 66 " pdb=" CG2 VAL D 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2687 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 195 " -0.025 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER N 195 " 0.092 2.00e-02 2.50e+03 pdb=" O SER N 195 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG N 196 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 526 " -0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG K 526 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 526 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 530 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C TRP L 530 " -0.053 2.00e-02 2.50e+03 pdb=" O TRP L 530 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP L 531 " 0.018 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 3712 2.79 - 3.49: 20724 3.49 - 4.20: 41531 4.20 - 4.90: 62984 Nonbonded interactions: 128958 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG L 522 " model vdw 1.379 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.686 3.120 nonbonded pdb=" O TRP K 530 " pdb=" CE3 TRP K 531 " model vdw 1.789 3.340 nonbonded pdb=" CG ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.796 3.350 nonbonded pdb=" OE1 GLU C 92 " pdb=" CZ ARG L 522 " model vdw 1.984 3.270 ... (remaining 128953 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' and resid 39 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 519 through 537) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 0.500 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 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 : 0.013 0.166 16702 Z= 0.905 Angle : 1.269 17.758 23819 Z= 0.913 Chirality : 0.067 0.372 2690 Planarity : 0.008 0.192 1986 Dihedral : 25.818 175.006 7028 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.28 % Favored : 89.21 % Rotamer: Outliers : 1.08 % Allowed : 6.16 % Favored : 92.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.36 (0.16), residues: 1196 helix: -4.62 (0.09), residues: 669 sheet: -2.35 (0.63), residues: 60 loop : -3.59 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 45 TYR 0.036 0.004 TYR H 37 PHE 0.045 0.004 PHE C 25 TRP 0.040 0.005 TRP N 28 HIS 0.013 0.003 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.01350 / 0.90 (16702) covalent geometry : angle 1.26941 / 0.91 (23819) hydrogen bonds : bond 0.32942 / 21.43 ( 478) hydrogen bonds : angle 12.06422 / 8.28 ( 1273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 331 time to evaluate : 0.482 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 43 VAL cc_start: 0.8069 (t) cc_final: 0.7848 (p) REVERT: B 84 MET cc_start: 0.7427 (mmm) cc_final: 0.6826 (mmm) REVERT: B 91 LYS cc_start: 0.8145 (tttm) cc_final: 0.7754 (ttpt) REVERT: C 16 SER cc_start: 0.8214 (m) cc_final: 0.7809 (p) REVERT: C 24 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7899 (mm-40) REVERT: C 36 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7397 (tmtt) REVERT: C 64 GLU cc_start: 0.8015 (tt0) cc_final: 0.7350 (tm-30) REVERT: C 84 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6644 (tp-100) REVERT: C 104 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8082 (mm-40) REVERT: D 42 TYR cc_start: 0.8123 (t80) cc_final: 0.7757 (t80) REVERT: D 76 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 85 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6925 (pttt) REVERT: E 48 LEU cc_start: 0.7826 (tt) cc_final: 0.7610 (tp) REVERT: E 56 LYS cc_start: 0.7009 (tttt) cc_final: 0.6477 (mmmm) REVERT: E 59 HIS cc_start: 0.8410 (m-70) cc_final: 0.8047 (m170) REVERT: E 68 SER cc_start: 0.8277 (t) cc_final: 0.8053 (m) REVERT: E 96 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 107 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6455 (tt0) REVERT: E 124 LYS cc_start: 0.7631 (mptm) cc_final: 0.7404 (mtpt) REVERT: F 44 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7123 (mtpt) REVERT: F 91 LYS cc_start: 0.7784 (tttp) cc_final: 0.7230 (ttmt) REVERT: F 93 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6306 (tp40) REVERT: G 36 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8303 (mmmm) REVERT: G 38 ASN cc_start: 0.8778 (m-40) cc_final: 0.8390 (m-40) REVERT: G 42 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6415 (mtp85) REVERT: G 73 ASN cc_start: 0.6898 (t160) cc_final: 0.6586 (t0) REVERT: G 95 LYS cc_start: 0.7173 (tmtm) cc_final: 0.6800 (mtpt) REVERT: H 38 SER cc_start: 0.8739 (p) cc_final: 0.8294 (t) REVERT: H 46 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7757 (mmtt) REVERT: H 71 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7316 (tm-30) REVERT: H 82 HIS cc_start: 0.7438 (t-90) cc_final: 0.7037 (t-90) REVERT: H 86 ARG cc_start: 0.7213 (mmt90) cc_final: 0.6497 (mtp180) REVERT: H 88 THR cc_start: 0.8392 (p) cc_final: 0.7975 (p) REVERT: H 93 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7203 (mt-10) REVERT: H 99 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7489 (mmm-85) REVERT: H 113 GLU cc_start: 0.7879 (tt0) cc_final: 0.7421 (tm-30) REVERT: L 526 ARG cc_start: 0.6671 (tpp80) cc_final: 0.6337 (mmm160) REVERT: L 527 PRO cc_start: 0.7722 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: M 1 MET cc_start: 0.2631 (ptt) cc_final: 0.2397 (ptp) REVERT: M 59 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7505 (mmtm) REVERT: M 69 LEU cc_start: 0.8622 (tp) cc_final: 0.8388 (tp) REVERT: N 1 MET cc_start: 0.0331 (ptt) cc_final: -0.0534 (mtm) REVERT: N 15 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7125 (ptmt) REVERT: N 74 MET cc_start: 0.7954 (tpp) cc_final: 0.7623 (tpt) REVERT: N 150 THR cc_start: 0.8516 (m) cc_final: 0.8029 (p) REVERT: N 165 SER cc_start: 0.6882 (m) cc_final: 0.6677 (m) outliers start: 11 outliers final: 2 residues processed: 339 average time/residue: 0.1738 time to fit residues: 79.5789 Evaluate side-chains 241 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain K residue 533 VAL Chi-restraints excluded: chain K residue 536 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN C 94 ASN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 38 ASN G 73 ASN G 94 ASN H 63 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN M 40 ASN M 129 ASN M 145 ASN N 19 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.177073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110477 restraints weight = 24849.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113560 restraints weight = 12628.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115458 restraints weight = 8940.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116450 restraints weight = 7596.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116851 restraints weight = 7059.338| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16702 Z= 0.314 Angle : 0.936 9.140 23819 Z= 0.517 Chirality : 0.056 0.329 2690 Planarity : 0.006 0.061 1986 Dihedral : 30.502 176.278 4656 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.87 % Favored : 89.97 % Rotamer: Outliers : 3.62 % Allowed : 12.13 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.19), residues: 1196 helix: -3.38 (0.14), residues: 688 sheet: -2.54 (0.59), residues: 64 loop : -3.44 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 526 TYR 0.032 0.003 TYR B 88 PHE 0.019 0.002 PHE F 100 TRP 0.047 0.003 TRP K 531 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.31 (16702) covalent geometry : angle 0.93577 / 0.52 (23819) hydrogen bonds : bond 0.09399 / 6.22 ( 478) hydrogen bonds : angle 5.91247 / 4.03 ( 1273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8917 (tttm) cc_final: 0.8536 (ttpt) REVERT: B 93 GLN cc_start: 0.8434 (tp40) cc_final: 0.7904 (tp40) REVERT: C 24 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8284 (mm-40) REVERT: C 36 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8126 (tmtt) REVERT: C 38 ASN cc_start: 0.8673 (t0) cc_final: 0.8103 (t0) REVERT: C 71 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7509 (mtm180) REVERT: C 95 LYS cc_start: 0.8894 (tptp) cc_final: 0.8538 (ttmt) REVERT: D 68 ASP cc_start: 0.8654 (t70) cc_final: 0.8186 (t0) REVERT: E 56 LYS cc_start: 0.7413 (tttt) cc_final: 0.7204 (mmmm) REVERT: E 60 LEU cc_start: 0.8898 (mp) cc_final: 0.8695 (mt) REVERT: E 108 ASP cc_start: 0.8548 (t0) cc_final: 0.8205 (t0) REVERT: E 136 GLU cc_start: 0.7318 (pm20) cc_final: 0.6966 (pm20) REVERT: F 44 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7473 (mtpt) REVERT: F 84 MET cc_start: 0.8569 (tpt) cc_final: 0.8127 (mmt) REVERT: F 91 LYS cc_start: 0.8560 (tttp) cc_final: 0.8076 (ttmt) REVERT: G 36 LYS cc_start: 0.9192 (mmpt) cc_final: 0.8811 (mmmm) REVERT: G 73 ASN cc_start: 0.8034 (t0) cc_final: 0.7784 (t0) REVERT: G 92 GLU cc_start: 0.8464 (mp0) cc_final: 0.8181 (mp0) REVERT: H 38 SER cc_start: 0.8860 (p) cc_final: 0.8559 (t) REVERT: H 46 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8735 (mppt) REVERT: H 82 HIS cc_start: 0.7747 (t-90) cc_final: 0.7522 (t-90) REVERT: H 86 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7695 (mtp180) REVERT: H 100 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8902 (mp) REVERT: H 113 GLU cc_start: 0.8293 (tt0) cc_final: 0.8028 (mt-10) REVERT: M 1 MET cc_start: 0.2380 (ptt) cc_final: 0.1418 (ptp) REVERT: M 28 TRP cc_start: 0.6606 (t60) cc_final: 0.6243 (t60) REVERT: M 51 HIS cc_start: 0.7759 (t-170) cc_final: 0.7073 (t-170) REVERT: M 54 HIS cc_start: 0.7039 (t70) cc_final: 0.6791 (t-90) REVERT: M 59 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7185 (mmtm) REVERT: M 137 TRP cc_start: 0.7182 (m100) cc_final: 0.6948 (m100) REVERT: N 1 MET cc_start: 0.0175 (ptt) cc_final: -0.0602 (mtm) REVERT: N 15 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7361 (ptmt) REVERT: N 78 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5778 (pm20) REVERT: N 151 TYR cc_start: 0.8079 (m-80) cc_final: 0.7709 (m-80) outliers start: 37 outliers final: 24 residues processed: 277 average time/residue: 0.1632 time to fit residues: 61.5701 Evaluate side-chains 238 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 122 optimal weight: 0.0770 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 78 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 95 GLN H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.180205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113441 restraints weight = 25157.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116813 restraints weight = 12760.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118876 restraints weight = 9005.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119989 restraints weight = 7633.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120419 restraints weight = 7075.215| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16702 Z= 0.157 Angle : 0.719 8.597 23819 Z= 0.411 Chirality : 0.046 0.316 2690 Planarity : 0.005 0.054 1986 Dihedral : 30.240 176.144 4651 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.42 % Allowed : 14.38 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.20), residues: 1196 helix: -2.61 (0.16), residues: 681 sheet: -2.51 (0.56), residues: 64 loop : -3.06 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.022 0.002 TYR B 51 PHE 0.014 0.002 PHE E 78 TRP 0.029 0.002 TRP M 28 HIS 0.009 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (16702) covalent geometry : angle 0.71919 / 0.41 (23819) hydrogen bonds : bond 0.07064 / 4.67 ( 478) hydrogen bonds : angle 4.86972 / 3.30 ( 1273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8817 (tp30) cc_final: 0.8561 (tp30) REVERT: B 91 LYS cc_start: 0.8868 (tttm) cc_final: 0.8452 (ttpt) REVERT: B 93 GLN cc_start: 0.8391 (tp40) cc_final: 0.8176 (tt0) REVERT: C 24 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8085 (mm-40) REVERT: C 36 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8024 (tmtt) REVERT: C 38 ASN cc_start: 0.8460 (t0) cc_final: 0.7764 (t0) REVERT: C 73 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8295 (t0) REVERT: C 95 LYS cc_start: 0.8895 (tptp) cc_final: 0.8443 (ttmt) REVERT: D 62 MET cc_start: 0.8992 (mmm) cc_final: 0.8663 (mmt) REVERT: D 68 ASP cc_start: 0.8573 (t70) cc_final: 0.7969 (t0) REVERT: E 136 GLU cc_start: 0.7349 (pm20) cc_final: 0.6965 (pm20) REVERT: F 44 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7311 (mtpt) REVERT: F 88 TYR cc_start: 0.8328 (m-10) cc_final: 0.7988 (m-10) REVERT: F 91 LYS cc_start: 0.8550 (tttp) cc_final: 0.7954 (ttmt) REVERT: G 35 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7892 (mtt-85) REVERT: G 36 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8727 (mmmm) REVERT: G 73 ASN cc_start: 0.7924 (t0) cc_final: 0.7625 (t0) REVERT: G 92 GLU cc_start: 0.8580 (mp0) cc_final: 0.8082 (mp0) REVERT: H 46 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8610 (mmtt) REVERT: H 67 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8400 (t0) REVERT: H 86 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7584 (mtp-110) REVERT: H 100 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8834 (mp) REVERT: H 113 GLU cc_start: 0.8032 (tt0) cc_final: 0.7767 (mt-10) REVERT: M 1 MET cc_start: 0.2639 (ptt) cc_final: 0.1737 (ptp) REVERT: M 16 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7728 (mp) REVERT: M 54 HIS cc_start: 0.6762 (t70) cc_final: 0.6561 (t-90) REVERT: M 59 LYS cc_start: 0.7507 (mtpp) cc_final: 0.7219 (mmtm) REVERT: M 148 LYS cc_start: 0.8475 (mttm) cc_final: 0.7933 (tppt) REVERT: N 1 MET cc_start: 0.0036 (ptt) cc_final: -0.0720 (mtm) REVERT: N 15 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7326 (ptmt) REVERT: N 78 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5743 (pm20) REVERT: N 165 SER cc_start: 0.6507 (m) cc_final: 0.5998 (t) outliers start: 35 outliers final: 18 residues processed: 256 average time/residue: 0.1561 time to fit residues: 54.8976 Evaluate side-chains 238 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain K residue 531 TRP Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN M 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.182632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117206 restraints weight = 24606.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120743 restraints weight = 11821.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122855 restraints weight = 8094.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123865 restraints weight = 6787.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124496 restraints weight = 6287.266| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16702 Z= 0.143 Angle : 0.667 9.180 23819 Z= 0.383 Chirality : 0.044 0.292 2690 Planarity : 0.004 0.052 1986 Dihedral : 30.127 175.914 4651 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.82 % Allowed : 14.97 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.21), residues: 1196 helix: -2.09 (0.17), residues: 688 sheet: -2.30 (0.58), residues: 64 loop : -2.95 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.021 0.002 TYR M 151 PHE 0.011 0.001 PHE B 100 TRP 0.024 0.002 TRP M 28 HIS 0.008 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (16702) covalent geometry : angle 0.66714 / 0.38 (23819) hydrogen bonds : bond 0.06226 / 4.09 ( 478) hydrogen bonds : angle 4.42920 / 3.00 ( 1273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.8725 (m-40) cc_final: 0.8403 (m-40) REVERT: B 91 LYS cc_start: 0.8838 (tttm) cc_final: 0.8443 (ttpt) REVERT: C 24 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8062 (mm-40) REVERT: C 36 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8021 (tmtt) REVERT: C 38 ASN cc_start: 0.8419 (t0) cc_final: 0.7633 (t0) REVERT: C 95 LYS cc_start: 0.8887 (tptp) cc_final: 0.8359 (ttmt) REVERT: D 62 MET cc_start: 0.9020 (mmm) cc_final: 0.8735 (mmt) REVERT: D 68 ASP cc_start: 0.8521 (t70) cc_final: 0.7961 (t0) REVERT: E 136 GLU cc_start: 0.7210 (pm20) cc_final: 0.6776 (mp0) REVERT: F 91 LYS cc_start: 0.8485 (tttp) cc_final: 0.7910 (ttmt) REVERT: G 36 LYS cc_start: 0.9119 (mmpt) cc_final: 0.8670 (mmmm) REVERT: G 73 ASN cc_start: 0.7953 (t0) cc_final: 0.7628 (t0) REVERT: G 92 GLU cc_start: 0.8539 (mp0) cc_final: 0.8072 (mp0) REVERT: H 46 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8727 (mmtt) REVERT: H 86 ARG cc_start: 0.8004 (mmt90) cc_final: 0.7634 (mtp-110) REVERT: M 1 MET cc_start: 0.2523 (ptt) cc_final: 0.1938 (ptp) REVERT: M 24 ILE cc_start: 0.7976 (mm) cc_final: 0.7747 (tp) REVERT: M 54 HIS cc_start: 0.6964 (t70) cc_final: 0.6757 (t70) REVERT: N 1 MET cc_start: -0.0044 (ptt) cc_final: -0.0675 (mtm) REVERT: N 78 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.5881 (pm20) REVERT: N 137 TRP cc_start: 0.8568 (m100) cc_final: 0.8158 (m100) REVERT: N 165 SER cc_start: 0.6687 (m) cc_final: 0.6471 (t) outliers start: 39 outliers final: 24 residues processed: 254 average time/residue: 0.1411 time to fit residues: 50.0973 Evaluate side-chains 237 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 10 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 79 optimal weight: 30.0000 chunk 141 optimal weight: 0.2980 chunk 103 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.175193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107005 restraints weight = 25128.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110252 restraints weight = 12684.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112193 restraints weight = 8937.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113217 restraints weight = 7573.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113610 restraints weight = 7027.124| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16702 Z= 0.284 Angle : 0.783 8.459 23819 Z= 0.430 Chirality : 0.049 0.311 2690 Planarity : 0.005 0.063 1986 Dihedral : 30.327 175.749 4651 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.53 % Favored : 90.30 % Rotamer: Outliers : 4.89 % Allowed : 16.73 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.22), residues: 1196 helix: -1.91 (0.18), residues: 698 sheet: -1.93 (0.64), residues: 64 loop : -3.14 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 92 TYR 0.023 0.002 TYR B 88 PHE 0.016 0.002 PHE E 122 TRP 0.021 0.003 TRP A 47 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.28 (16702) covalent geometry : angle 0.78332 / 0.43 (23819) hydrogen bonds : bond 0.06667 / 4.43 ( 478) hydrogen bonds : angle 4.71442 / 3.24 ( 1273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8920 (mt0) cc_final: 0.8716 (mt0) REVERT: B 91 LYS cc_start: 0.8976 (tttm) cc_final: 0.8581 (ttpt) REVERT: C 24 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8144 (mm-40) REVERT: C 36 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8171 (tmtt) REVERT: C 38 ASN cc_start: 0.8408 (t0) cc_final: 0.7303 (t0) REVERT: C 64 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 73 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8362 (t0) REVERT: C 95 LYS cc_start: 0.8944 (tptp) cc_final: 0.8424 (ttmt) REVERT: D 62 MET cc_start: 0.9009 (mmm) cc_final: 0.8630 (mmt) REVERT: D 68 ASP cc_start: 0.8755 (t70) cc_final: 0.8257 (t0) REVERT: E 136 GLU cc_start: 0.7125 (pm20) cc_final: 0.6890 (pm20) REVERT: F 52 GLU cc_start: 0.7886 (tp30) cc_final: 0.7536 (tp30) REVERT: F 91 LYS cc_start: 0.8642 (tttp) cc_final: 0.8095 (ttmt) REVERT: G 36 LYS cc_start: 0.9220 (mmpt) cc_final: 0.8778 (mmmm) REVERT: G 38 ASN cc_start: 0.8412 (t0) cc_final: 0.7952 (t0) REVERT: G 75 LYS cc_start: 0.7784 (mttm) cc_final: 0.7464 (mttp) REVERT: G 92 GLU cc_start: 0.8603 (mp0) cc_final: 0.8209 (mp0) REVERT: H 46 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8707 (mmtt) REVERT: H 86 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7705 (mtp180) REVERT: H 120 LYS cc_start: 0.7423 (tttt) cc_final: 0.7219 (tttm) REVERT: L 522 ARG cc_start: 0.8791 (ptt90) cc_final: 0.8532 (ptt90) REVERT: M 1 MET cc_start: 0.2568 (ptt) cc_final: 0.1967 (ptp) REVERT: M 24 ILE cc_start: 0.8076 (mm) cc_final: 0.7842 (tp) REVERT: N 1 MET cc_start: 0.0132 (ptt) cc_final: -0.0569 (mtm) REVERT: N 78 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5856 (pm20) outliers start: 50 outliers final: 41 residues processed: 250 average time/residue: 0.1493 time to fit residues: 51.9677 Evaluate side-chains 243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 531 TRP Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 10 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 95 optimal weight: 20.0000 chunk 15 optimal weight: 0.0770 chunk 143 optimal weight: 0.0570 chunk 91 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 0.0770 chunk 131 optimal weight: 4.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116162 restraints weight = 24748.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120198 restraints weight = 12361.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120506 restraints weight = 7801.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120765 restraints weight = 7962.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120910 restraints weight = 7588.659| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 16702 Z= 0.137 Angle : 0.648 8.751 23819 Z= 0.372 Chirality : 0.043 0.295 2690 Planarity : 0.004 0.058 1986 Dihedral : 30.024 176.486 4651 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.13 % Allowed : 19.08 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.22), residues: 1196 helix: -1.44 (0.19), residues: 674 sheet: -1.96 (0.64), residues: 64 loop : -2.74 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 36 TYR 0.016 0.001 TYR B 88 PHE 0.016 0.001 PHE B 100 TRP 0.021 0.002 TRP M 137 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (16702) covalent geometry : angle 0.64806 / 0.37 (23819) hydrogen bonds : bond 0.05653 / 3.70 ( 478) hydrogen bonds : angle 4.15381 / 2.81 ( 1273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8658 (tttm) cc_final: 0.8292 (ttpt) REVERT: C 24 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8332 (mm-40) REVERT: C 36 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8065 (tmtt) REVERT: C 38 ASN cc_start: 0.8283 (t0) cc_final: 0.7705 (t0) REVERT: C 73 ASN cc_start: 0.8510 (t0) cc_final: 0.7858 (t0) REVERT: C 95 LYS cc_start: 0.8947 (tptp) cc_final: 0.8381 (ttmt) REVERT: D 62 MET cc_start: 0.9029 (mmm) cc_final: 0.8748 (mmt) REVERT: D 68 ASP cc_start: 0.8520 (t70) cc_final: 0.7986 (t0) REVERT: F 91 LYS cc_start: 0.8515 (tttp) cc_final: 0.8068 (ttmt) REVERT: G 36 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8681 (mmmm) REVERT: G 92 GLU cc_start: 0.8508 (mp0) cc_final: 0.8298 (mp0) REVERT: H 46 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8708 (mmtt) REVERT: H 68 ASP cc_start: 0.7936 (t70) cc_final: 0.7256 (t0) REVERT: H 86 ARG cc_start: 0.8030 (mmt90) cc_final: 0.7590 (mtp180) REVERT: H 120 LYS cc_start: 0.7308 (tttt) cc_final: 0.6910 (tttp) REVERT: K 529 ASP cc_start: 0.7743 (t0) cc_final: 0.7459 (t0) REVERT: L 522 ARG cc_start: 0.8767 (ptt90) cc_final: 0.8504 (ptt90) REVERT: M 1 MET cc_start: 0.2516 (ptt) cc_final: 0.1944 (ptp) REVERT: N 1 MET cc_start: -0.0066 (ptt) cc_final: -0.0757 (mtt) REVERT: N 78 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: N 137 TRP cc_start: 0.8499 (m100) cc_final: 0.8272 (m100) outliers start: 32 outliers final: 20 residues processed: 244 average time/residue: 0.1444 time to fit residues: 49.1931 Evaluate side-chains 238 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 10 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 145 ASN M 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.180323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113556 restraints weight = 24546.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116658 restraints weight = 12874.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118560 restraints weight = 9253.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119534 restraints weight = 7918.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119842 restraints weight = 7392.405| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16702 Z= 0.151 Angle : 0.651 8.250 23819 Z= 0.368 Chirality : 0.042 0.294 2690 Planarity : 0.004 0.060 1986 Dihedral : 29.991 176.162 4651 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.13 % Allowed : 19.77 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.23), residues: 1196 helix: -1.20 (0.19), residues: 677 sheet: -1.81 (0.64), residues: 64 loop : -2.70 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 131 TYR 0.018 0.001 TYR N 73 PHE 0.013 0.001 PHE M 8 TRP 0.021 0.002 TRP M 137 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (16702) covalent geometry : angle 0.65076 / 0.37 (23819) hydrogen bonds : bond 0.05629 / 3.69 ( 478) hydrogen bonds : angle 4.03177 / 2.74 ( 1273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8818 (tttm) cc_final: 0.8411 (ttpt) REVERT: C 24 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8383 (mm-40) REVERT: C 36 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8073 (tmtt) REVERT: C 38 ASN cc_start: 0.8389 (t0) cc_final: 0.6721 (t0) REVERT: C 41 GLU cc_start: 0.7606 (tp30) cc_final: 0.7398 (tp30) REVERT: C 73 ASN cc_start: 0.8729 (t0) cc_final: 0.8223 (t0) REVERT: C 95 LYS cc_start: 0.9006 (tptp) cc_final: 0.8375 (ttmt) REVERT: D 35 GLU cc_start: 0.7833 (pt0) cc_final: 0.7065 (pm20) REVERT: D 68 ASP cc_start: 0.8636 (t70) cc_final: 0.8056 (t0) REVERT: F 44 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7582 (mtpt) REVERT: F 52 GLU cc_start: 0.7779 (tp30) cc_final: 0.7390 (tp30) REVERT: F 91 LYS cc_start: 0.8580 (tttp) cc_final: 0.8094 (ttmt) REVERT: G 36 LYS cc_start: 0.9188 (mmpt) cc_final: 0.8685 (mmmm) REVERT: G 38 ASN cc_start: 0.8407 (t0) cc_final: 0.7811 (t0) REVERT: G 75 LYS cc_start: 0.7683 (mttm) cc_final: 0.7408 (mttp) REVERT: H 46 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8635 (mppt) REVERT: H 68 ASP cc_start: 0.8049 (t70) cc_final: 0.7325 (t0) REVERT: H 86 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7614 (mtp180) REVERT: K 529 ASP cc_start: 0.7856 (t0) cc_final: 0.7556 (t0) REVERT: M 1 MET cc_start: 0.2324 (ptt) cc_final: 0.1731 (ptp) REVERT: M 137 TRP cc_start: 0.7049 (m100) cc_final: 0.6777 (m100) REVERT: N 1 MET cc_start: -0.0015 (ptt) cc_final: -0.0651 (mtt) REVERT: N 78 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5853 (pm20) outliers start: 32 outliers final: 21 residues processed: 240 average time/residue: 0.1364 time to fit residues: 46.6941 Evaluate side-chains 236 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 120 optimal weight: 0.2980 chunk 88 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 122 optimal weight: 0.2980 chunk 144 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS B 93 GLN D 84 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.179800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113085 restraints weight = 24741.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116288 restraints weight = 12529.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118223 restraints weight = 8847.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119136 restraints weight = 7507.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119708 restraints weight = 6990.875| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16702 Z= 0.184 Angle : 0.674 12.986 23819 Z= 0.376 Chirality : 0.043 0.299 2690 Planarity : 0.004 0.062 1986 Dihedral : 29.966 175.643 4651 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.52 % Allowed : 19.47 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.23), residues: 1196 helix: -1.03 (0.19), residues: 677 sheet: -1.83 (0.63), residues: 64 loop : -2.61 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 131 TYR 0.017 0.002 TYR F 88 PHE 0.011 0.001 PHE B 100 TRP 0.018 0.002 TRP K 530 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (16702) covalent geometry : angle 0.67435 / 0.38 (23819) hydrogen bonds : bond 0.05552 / 3.64 ( 478) hydrogen bonds : angle 4.11731 / 2.82 ( 1273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.471 Fit side-chains REVERT: B 91 LYS cc_start: 0.8762 (tttm) cc_final: 0.8405 (ttpt) REVERT: C 24 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8315 (mm-40) REVERT: C 36 LYS cc_start: 0.8430 (mmmt) cc_final: 0.8152 (tmtt) REVERT: C 38 ASN cc_start: 0.8437 (t0) cc_final: 0.6960 (t0) REVERT: C 73 ASN cc_start: 0.8608 (t0) cc_final: 0.7943 (t0) REVERT: C 95 LYS cc_start: 0.9022 (tptp) cc_final: 0.8407 (ttmt) REVERT: D 35 GLU cc_start: 0.7965 (pt0) cc_final: 0.7211 (pm20) REVERT: D 59 MET cc_start: 0.8709 (tpt) cc_final: 0.8306 (tpt) REVERT: D 68 ASP cc_start: 0.8607 (t70) cc_final: 0.8068 (t0) REVERT: D 71 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7875 (tm-30) REVERT: F 25 ASN cc_start: 0.8002 (t0) cc_final: 0.7766 (t0) REVERT: F 44 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7629 (mtpt) REVERT: F 52 GLU cc_start: 0.7835 (tp30) cc_final: 0.7453 (tp30) REVERT: F 91 LYS cc_start: 0.8629 (tttp) cc_final: 0.8149 (ttmt) REVERT: G 36 LYS cc_start: 0.9162 (mmpt) cc_final: 0.8689 (mmmm) REVERT: G 38 ASN cc_start: 0.8343 (t0) cc_final: 0.8114 (t0) REVERT: G 75 LYS cc_start: 0.7727 (mttm) cc_final: 0.7450 (mttp) REVERT: G 92 GLU cc_start: 0.8436 (mp0) cc_final: 0.7721 (mp0) REVERT: H 46 LYS cc_start: 0.9007 (mmtp) cc_final: 0.8756 (mppt) REVERT: H 68 ASP cc_start: 0.8008 (t70) cc_final: 0.7306 (t0) REVERT: H 86 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7687 (mtp180) REVERT: K 529 ASP cc_start: 0.7589 (t0) cc_final: 0.7123 (t0) REVERT: M 1 MET cc_start: 0.2326 (ptt) cc_final: 0.1707 (ptp) REVERT: M 137 TRP cc_start: 0.7160 (m100) cc_final: 0.6854 (m100) REVERT: M 148 LYS cc_start: 0.8392 (mttt) cc_final: 0.8108 (mttm) REVERT: N 1 MET cc_start: 0.0040 (ptt) cc_final: -0.0587 (mtt) REVERT: N 78 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.5899 (pm20) REVERT: N 137 TRP cc_start: 0.8285 (m100) cc_final: 0.7898 (m100) outliers start: 36 outliers final: 26 residues processed: 240 average time/residue: 0.1422 time to fit residues: 48.0955 Evaluate side-chains 242 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 533 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 158 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.0020 chunk 76 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 138 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.182406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116689 restraints weight = 24621.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119719 restraints weight = 12787.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121615 restraints weight = 9160.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122448 restraints weight = 7818.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122924 restraints weight = 7318.709| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16702 Z= 0.139 Angle : 0.636 12.044 23819 Z= 0.359 Chirality : 0.041 0.292 2690 Planarity : 0.004 0.059 1986 Dihedral : 29.785 176.104 4651 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.25 % Allowed : 21.04 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.23), residues: 1196 helix: -0.78 (0.20), residues: 677 sheet: -1.80 (0.66), residues: 64 loop : -2.56 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 522 TYR 0.021 0.001 TYR F 88 PHE 0.016 0.001 PHE M 8 TRP 0.018 0.002 TRP N 83 HIS 0.004 0.001 HIS M 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (16702) covalent geometry : angle 0.63566 / 0.36 (23819) hydrogen bonds : bond 0.05265 / 3.42 ( 478) hydrogen bonds : angle 3.88137 / 2.65 ( 1273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9027 (tp) REVERT: B 91 LYS cc_start: 0.8843 (tttm) cc_final: 0.8419 (ttpt) REVERT: B 96 THR cc_start: 0.8953 (m) cc_final: 0.8732 (p) REVERT: C 24 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8329 (mm-40) REVERT: C 36 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8090 (tmtt) REVERT: C 38 ASN cc_start: 0.8474 (t0) cc_final: 0.6951 (t0) REVERT: C 73 ASN cc_start: 0.8712 (t0) cc_final: 0.8036 (t0) REVERT: C 95 LYS cc_start: 0.9032 (tptp) cc_final: 0.8384 (ttmt) REVERT: D 35 GLU cc_start: 0.7933 (pt0) cc_final: 0.7274 (pm20) REVERT: D 68 ASP cc_start: 0.8623 (t70) cc_final: 0.8037 (t0) REVERT: F 44 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7557 (mtpt) REVERT: F 52 GLU cc_start: 0.7759 (tp30) cc_final: 0.7371 (tp30) REVERT: F 91 LYS cc_start: 0.8632 (tttp) cc_final: 0.8117 (ttmt) REVERT: G 36 LYS cc_start: 0.9162 (mmpt) cc_final: 0.8718 (mmmm) REVERT: G 38 ASN cc_start: 0.8433 (t0) cc_final: 0.7932 (t0) REVERT: G 92 GLU cc_start: 0.8474 (mp0) cc_final: 0.7580 (mp0) REVERT: H 46 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8726 (tppt) REVERT: H 68 ASP cc_start: 0.7980 (t70) cc_final: 0.7248 (t0) REVERT: H 86 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7448 (mtp180) REVERT: K 529 ASP cc_start: 0.7623 (t0) cc_final: 0.7003 (t0) REVERT: L 522 ARG cc_start: 0.8765 (ptt90) cc_final: 0.8556 (ptt90) REVERT: M 1 MET cc_start: 0.2189 (ptt) cc_final: 0.1599 (ptp) REVERT: M 137 TRP cc_start: 0.7093 (m100) cc_final: 0.6860 (m100) REVERT: M 148 LYS cc_start: 0.8394 (mttt) cc_final: 0.8122 (mttm) REVERT: N 1 MET cc_start: -0.0083 (ptt) cc_final: -0.0679 (mtt) REVERT: N 11 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8624 (ttm-80) REVERT: N 78 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5889 (pm20) outliers start: 23 outliers final: 18 residues processed: 231 average time/residue: 0.1447 time to fit residues: 47.1429 Evaluate side-chains 232 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS M 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.179107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112421 restraints weight = 24641.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115722 restraints weight = 12022.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117687 restraints weight = 8355.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118715 restraints weight = 7058.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118948 restraints weight = 6546.379| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16702 Z= 0.190 Angle : 0.672 12.318 23819 Z= 0.374 Chirality : 0.043 0.297 2690 Planarity : 0.004 0.061 1986 Dihedral : 29.850 175.440 4651 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.25 % Allowed : 21.72 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.23), residues: 1196 helix: -0.76 (0.20), residues: 674 sheet: -1.85 (0.65), residues: 64 loop : -2.53 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 522 TYR 0.017 0.002 TYR F 88 PHE 0.010 0.001 PHE B 100 TRP 0.013 0.002 TRP N 83 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (16702) covalent geometry : angle 0.67201 / 0.37 (23819) hydrogen bonds : bond 0.05473 / 3.58 ( 478) hydrogen bonds : angle 4.01367 / 2.76 ( 1273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9058 (tp) REVERT: B 44 LYS cc_start: 0.8430 (tttt) cc_final: 0.7972 (tttt) REVERT: B 91 LYS cc_start: 0.8845 (tttm) cc_final: 0.8376 (ttpt) REVERT: C 36 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8156 (tmtt) REVERT: C 38 ASN cc_start: 0.8500 (t0) cc_final: 0.6982 (t0) REVERT: C 64 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 73 ASN cc_start: 0.8632 (t0) cc_final: 0.7987 (t0) REVERT: C 95 LYS cc_start: 0.9049 (tptp) cc_final: 0.8395 (ttmt) REVERT: D 35 GLU cc_start: 0.8007 (pt0) cc_final: 0.7256 (pm20) REVERT: D 68 ASP cc_start: 0.8678 (t70) cc_final: 0.8101 (t0) REVERT: F 25 ASN cc_start: 0.8042 (t0) cc_final: 0.7842 (t0) REVERT: F 52 GLU cc_start: 0.7890 (tp30) cc_final: 0.7560 (tp30) REVERT: F 91 LYS cc_start: 0.8642 (tttp) cc_final: 0.8173 (ttmt) REVERT: G 36 LYS cc_start: 0.9169 (mmpt) cc_final: 0.8738 (mmmm) REVERT: G 38 ASN cc_start: 0.8455 (t0) cc_final: 0.7991 (t0) REVERT: G 75 LYS cc_start: 0.7719 (mttm) cc_final: 0.7420 (mttp) REVERT: G 92 GLU cc_start: 0.8459 (mp0) cc_final: 0.7617 (mp0) REVERT: H 46 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8698 (tppt) REVERT: H 68 ASP cc_start: 0.8163 (t70) cc_final: 0.7329 (t0) REVERT: H 86 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7541 (mtp180) REVERT: K 529 ASP cc_start: 0.7653 (t0) cc_final: 0.7080 (t0) REVERT: K 536 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4440 (tt0) REVERT: L 522 ARG cc_start: 0.8676 (ptt90) cc_final: 0.8456 (ptt90) REVERT: M 1 MET cc_start: 0.2176 (ptt) cc_final: 0.1570 (ptp) REVERT: M 148 LYS cc_start: 0.8466 (mttt) cc_final: 0.8195 (mttm) REVERT: N 1 MET cc_start: -0.0068 (ptt) cc_final: -0.0592 (mtt) REVERT: N 11 ARG cc_start: 0.8857 (ttm-80) cc_final: 0.8645 (ttm-80) REVERT: N 78 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5905 (pm20) outliers start: 23 outliers final: 19 residues processed: 230 average time/residue: 0.1461 time to fit residues: 47.3601 Evaluate side-chains 234 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 0.7980 chunk 137 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116004 restraints weight = 24653.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119274 restraints weight = 12297.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121250 restraints weight = 8597.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122227 restraints weight = 7277.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122635 restraints weight = 6753.749| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16702 Z= 0.135 Angle : 0.628 13.198 23819 Z= 0.356 Chirality : 0.041 0.290 2690 Planarity : 0.004 0.060 1986 Dihedral : 29.697 175.746 4651 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.25 % Allowed : 21.43 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.23), residues: 1196 helix: -0.57 (0.20), residues: 683 sheet: -1.74 (0.66), residues: 64 loop : -2.51 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 522 TYR 0.023 0.001 TYR H 83 PHE 0.016 0.001 PHE M 8 TRP 0.050 0.002 TRP M 137 HIS 0.005 0.001 HIS M 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (16702) covalent geometry : angle 0.62822 / 0.36 (23819) hydrogen bonds : bond 0.05198 / 3.38 ( 478) hydrogen bonds : angle 3.80610 / 2.59 ( 1273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.33 seconds wall clock time: 50 minutes 55.58 seconds (3055.58 seconds total)