Starting phenix.real_space_refine on Wed Mar 4 18:09:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mup_9251/03_2026/6mup_9251.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mup_9251/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mup_9251/03_2026/6mup_9251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mup_9251/03_2026/6mup_9251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mup_9251/03_2026/6mup_9251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mup_9251/03_2026/6mup_9251.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5986/lib/python3.9/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: 2.99, 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: 1.07 Conformation dependent library (CDL) restraints added in 337.5 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: 2.06 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=" N PRO K 527 " pdb=" CD PRO K 527 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C LEU H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.25e-02 6.40e+03 9.62e+00 bond pdb=" CB THR E 113 " pdb=" CG2 THR E 113 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.19e+00 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 23425 3.55 - 7.10: 360 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=" 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 angle pdb=" C ARG K 521 " pdb=" N ARG K 522 " pdb=" CA ARG K 522 " ideal model delta sigma weight residual 122.93 132.61 -9.68 1.45e+00 4.76e-01 4.46e+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: 2152 0.074 - 0.149: 489 0.149 - 0.223: 39 0.223 - 0.297: 9 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: 0.760 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.160 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 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= 0.582 Angle : 1.189 17.758 23819 Z= 0.685 Chirality : 0.061 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 covalent geometry : bond 0.01308 (16702) covalent geometry : angle 1.18924 (23819) hydrogen bonds : bond 0.32942 ( 478) hydrogen bonds : angle 12.06422 ( 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 : 0.402 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: 0.7351 (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: 0.7802 (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: 0.7229 (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: 0.6588 (t0) REVERT: G 76 THR cc_start: 0.7617 (p) cc_final: 0.7253 (t) 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: 0.7204 (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: 0.7422 (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: 0.8389 (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: 0.6678 (m) outliers start: 11 outliers final: 2 residues processed: 339 average time/residue: 0.1680 time to fit residues: 75.9367 Evaluate side-chains 240 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 3.9990 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: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.178262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113077 restraints weight = 24718.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116092 restraints weight = 12607.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117975 restraints weight = 8912.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118917 restraints weight = 7568.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119314 restraints weight = 7027.115| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16702 Z= 0.237 Angle : 0.736 7.530 23819 Z= 0.419 Chirality : 0.041 0.281 2690 Planarity : 0.005 0.063 1986 Dihedral : 30.067 173.627 4656 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.19 % Favored : 91.64 % Rotamer: Outliers : 3.42 % Allowed : 11.64 % Favored : 84.93 % 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: -4.95 (0.19), residues: 1196 helix: -3.21 (0.14), residues: 682 sheet: -2.30 (0.61), residues: 64 loop : -3.30 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 526 TYR 0.025 0.002 TYR B 51 PHE 0.012 0.002 PHE F 100 TRP 0.025 0.002 TRP K 531 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (16702) covalent geometry : angle 0.73604 (23819) hydrogen bonds : bond 0.06835 ( 478) hydrogen bonds : angle 5.21938 ( 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 302 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8572 (mtm110) cc_final: 0.8253 (mtm110) REVERT: A 83 ASP cc_start: 0.8173 (p0) cc_final: 0.7938 (p0) REVERT: B 91 LYS cc_start: 0.8868 (tttm) cc_final: 0.8520 (ttpt) REVERT: B 93 GLN cc_start: 0.8354 (tp40) cc_final: 0.7720 (tp40) REVERT: C 24 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8152 (mm-40) REVERT: C 36 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8144 (tmtt) REVERT: C 38 ASN cc_start: 0.8654 (t0) cc_final: 0.8091 (t0) REVERT: C 95 LYS cc_start: 0.8928 (tptp) cc_final: 0.8513 (ttmt) REVERT: D 59 MET cc_start: 0.8583 (tpp) cc_final: 0.8330 (mmm) REVERT: D 68 ASP cc_start: 0.8591 (t70) cc_final: 0.8107 (t0) REVERT: E 136 GLU cc_start: 0.7153 (pm20) cc_final: 0.6853 (pm20) REVERT: F 44 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7495 (mtpt) REVERT: F 84 MET cc_start: 0.8389 (tpt) cc_final: 0.8155 (mmt) REVERT: F 91 LYS cc_start: 0.8463 (tttp) cc_final: 0.8003 (ttmt) REVERT: G 36 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8730 (mmmm) REVERT: G 61 GLU cc_start: 0.8418 (tp30) cc_final: 0.8159 (tp30) REVERT: G 73 ASN cc_start: 0.7985 (t0) cc_final: 0.7692 (t0) REVERT: G 76 THR cc_start: 0.9084 (p) cc_final: 0.8743 (t) REVERT: G 92 GLU cc_start: 0.8440 (mp0) cc_final: 0.8124 (mp0) REVERT: H 86 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7634 (mtp180) REVERT: H 100 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8945 (mp) REVERT: M 1 MET cc_start: 0.2244 (ptt) cc_final: 0.1192 (ptp) REVERT: M 148 LYS cc_start: 0.8598 (mttm) cc_final: 0.8091 (mttp) REVERT: N 1 MET cc_start: 0.0327 (ptt) cc_final: -0.0436 (mtm) REVERT: N 15 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7422 (ptmt) REVERT: N 78 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5929 (pm20) REVERT: N 151 TYR cc_start: 0.8063 (m-80) cc_final: 0.7584 (m-80) outliers start: 35 outliers final: 18 residues processed: 286 average time/residue: 0.1602 time to fit residues: 61.8589 Evaluate side-chains 231 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 38 SER 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 H residue 66 VAL 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 120 THR Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 78 GLN 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: 6.9990 chunk 80 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105817 restraints weight = 25398.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108841 restraints weight = 13367.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110710 restraints weight = 9635.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111648 restraints weight = 8251.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112123 restraints weight = 7698.948| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 16702 Z= 0.297 Angle : 0.736 6.669 23819 Z= 0.415 Chirality : 0.042 0.240 2690 Planarity : 0.005 0.064 1986 Dihedral : 30.022 173.582 4651 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.78 % Favored : 90.05 % Rotamer: Outliers : 4.79 % Allowed : 14.68 % Favored : 80.53 % 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: -4.14 (0.20), residues: 1196 helix: -2.38 (0.17), residues: 681 sheet: -2.10 (0.60), residues: 64 loop : -3.24 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 35 TYR 0.014 0.002 TYR H 83 PHE 0.020 0.002 PHE C 25 TRP 0.022 0.002 TRP A 47 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00678 (16702) covalent geometry : angle 0.73623 (23819) hydrogen bonds : bond 0.06012 ( 478) hydrogen bonds : angle 4.85788 ( 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 277 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5675 (ttt-90) REVERT: B 91 LYS cc_start: 0.8892 (tttm) cc_final: 0.8481 (ttpt) REVERT: C 36 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8180 (tmtt) REVERT: C 38 ASN cc_start: 0.8687 (t0) cc_final: 0.8135 (t0) REVERT: C 73 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7386 (t0) REVERT: C 95 LYS cc_start: 0.8973 (tptp) cc_final: 0.8434 (ttmt) REVERT: D 62 MET cc_start: 0.9097 (mmm) cc_final: 0.8629 (mmt) REVERT: D 68 ASP cc_start: 0.8665 (t70) cc_final: 0.8156 (t0) REVERT: E 58 THR cc_start: 0.9336 (p) cc_final: 0.9121 (p) REVERT: E 96 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7876 (mt-10) REVERT: E 136 GLU cc_start: 0.6968 (pm20) cc_final: 0.6685 (pm20) REVERT: F 52 GLU cc_start: 0.7863 (tp30) cc_final: 0.7583 (tp30) REVERT: F 91 LYS cc_start: 0.8606 (tttp) cc_final: 0.8188 (ttmt) REVERT: G 36 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8703 (mmmm) REVERT: G 75 LYS cc_start: 0.7968 (mttt) cc_final: 0.7669 (mttp) REVERT: G 76 THR cc_start: 0.9084 (p) cc_final: 0.8744 (t) REVERT: G 92 GLU cc_start: 0.8508 (mp0) cc_final: 0.8277 (mp0) REVERT: H 68 ASP cc_start: 0.8052 (t70) cc_final: 0.7321 (t0) REVERT: H 86 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7713 (mtp180) REVERT: K 529 ASP cc_start: 0.8119 (t0) cc_final: 0.7834 (t0) REVERT: K 534 LYS cc_start: 0.4260 (OUTLIER) cc_final: 0.4027 (tmmt) REVERT: K 536 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4695 (tt0) REVERT: L 526 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7739 (tpp80) REVERT: M 1 MET cc_start: 0.2459 (ptt) cc_final: 0.1369 (ptp) REVERT: M 70 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (t0) REVERT: M 148 LYS cc_start: 0.8557 (mttm) cc_final: 0.8048 (mttp) REVERT: N 1 MET cc_start: 0.0097 (ptt) cc_final: -0.0603 (mtm) REVERT: N 78 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5894 (pm20) outliers start: 49 outliers final: 29 residues processed: 260 average time/residue: 0.1556 time to fit residues: 54.7320 Evaluate side-chains 234 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 74 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 27 VAL 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 38 SER Chi-restraints excluded: chain D residue 48 VAL 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 82 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 534 LYS Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 133 ILE 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 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 153 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: 3.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN C 73 ASN D 47 GLN D 84 ASN G 38 ASN H 67 ASN M 54 HIS ** M 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 145 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.180386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117115 restraints weight = 24610.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118455 restraints weight = 13603.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120469 restraints weight = 8891.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120703 restraints weight = 7893.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120454 restraints weight = 7252.540| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16702 Z= 0.156 Angle : 0.610 7.122 23819 Z= 0.354 Chirality : 0.037 0.186 2690 Planarity : 0.004 0.060 1986 Dihedral : 29.601 173.085 4651 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.01 % Allowed : 16.34 % Favored : 79.65 % 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: -3.35 (0.22), residues: 1196 helix: -1.74 (0.18), residues: 685 sheet: -1.77 (0.65), residues: 64 loop : -2.93 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 133 TYR 0.014 0.001 TYR B 51 PHE 0.011 0.001 PHE B 100 TRP 0.021 0.002 TRP A 47 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (16702) covalent geometry : angle 0.61002 (23819) hydrogen bonds : bond 0.05040 ( 478) hydrogen bonds : angle 4.13140 ( 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 277 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8030 (p0) cc_final: 0.7720 (p0) REVERT: B 91 LYS cc_start: 0.8885 (tttm) cc_final: 0.8425 (ttpt) REVERT: C 24 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8143 (mm-40) REVERT: C 36 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8139 (tmtt) REVERT: C 38 ASN cc_start: 0.8619 (t0) cc_final: 0.7894 (t0) REVERT: C 73 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7475 (t0) REVERT: C 95 LYS cc_start: 0.9033 (tptp) cc_final: 0.8443 (ttmt) REVERT: D 37 TYR cc_start: 0.8911 (m-80) cc_final: 0.8696 (m-80) REVERT: D 42 TYR cc_start: 0.8610 (t80) cc_final: 0.8344 (t80) REVERT: D 68 ASP cc_start: 0.8459 (t70) cc_final: 0.7913 (t0) REVERT: E 96 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7809 (mt-10) REVERT: F 52 GLU cc_start: 0.7902 (tp30) cc_final: 0.7503 (tp30) REVERT: F 88 TYR cc_start: 0.8210 (m-10) cc_final: 0.7952 (m-10) REVERT: F 91 LYS cc_start: 0.8514 (tttp) cc_final: 0.8073 (ttmt) REVERT: G 36 LYS cc_start: 0.9095 (mmpt) cc_final: 0.8604 (mmmm) REVERT: G 61 GLU cc_start: 0.8308 (tp30) cc_final: 0.8096 (tp30) REVERT: G 76 THR cc_start: 0.9046 (p) cc_final: 0.8828 (t) REVERT: G 95 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8471 (mtpp) REVERT: H 68 ASP cc_start: 0.8063 (t70) cc_final: 0.7362 (t0) REVERT: H 86 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7496 (mtp180) REVERT: H 120 LYS cc_start: 0.7316 (tttt) cc_final: 0.7108 (tptt) REVERT: K 529 ASP cc_start: 0.7807 (t0) cc_final: 0.7413 (t0) REVERT: K 536 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4491 (tt0) REVERT: M 1 MET cc_start: 0.2249 (ptt) cc_final: 0.1193 (ptp) REVERT: N 1 MET cc_start: -0.0155 (ptt) cc_final: -0.0670 (mtm) REVERT: N 11 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8448 (ttm-80) REVERT: N 78 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5852 (pm20) outliers start: 41 outliers final: 20 residues processed: 263 average time/residue: 0.1451 time to fit residues: 52.9527 Evaluate side-chains 236 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR 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 93 GLN Chi-restraints excluded: chain H residue 111 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 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 79 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN H 67 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 = 0.4251 r_free = 0.4251 target = 0.176898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110334 restraints weight = 24812.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113555 restraints weight = 12297.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115464 restraints weight = 8575.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116383 restraints weight = 7248.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116708 restraints weight = 6739.892| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16702 Z= 0.240 Angle : 0.661 8.459 23819 Z= 0.375 Chirality : 0.039 0.191 2690 Planarity : 0.004 0.065 1986 Dihedral : 29.706 171.168 4651 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 4.11 % Allowed : 19.08 % Favored : 76.81 % 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: -3.09 (0.22), residues: 1196 helix: -1.50 (0.19), residues: 669 sheet: -1.52 (0.68), residues: 64 loop : -2.86 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 131 TYR 0.041 0.002 TYR H 83 PHE 0.015 0.001 PHE C 25 TRP 0.019 0.002 TRP M 28 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00545 (16702) covalent geometry : angle 0.66076 (23819) hydrogen bonds : bond 0.05267 ( 478) hydrogen bonds : angle 4.27504 ( 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 264 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8667 (m-30) cc_final: 0.8356 (m-30) REVERT: B 84 MET cc_start: 0.8142 (tpp) cc_final: 0.7877 (mmt) REVERT: B 91 LYS cc_start: 0.8896 (tttm) cc_final: 0.8548 (ttpt) REVERT: B 92 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8402 (ttp80) REVERT: C 36 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8144 (tmtt) REVERT: C 38 ASN cc_start: 0.8746 (t0) cc_final: 0.7130 (t0) REVERT: C 64 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 73 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7547 (t0) REVERT: C 95 LYS cc_start: 0.9069 (tptp) cc_final: 0.8417 (ttmt) REVERT: D 68 ASP cc_start: 0.8696 (t70) cc_final: 0.8141 (t0) REVERT: E 58 THR cc_start: 0.9318 (p) cc_final: 0.9082 (p) REVERT: E 131 ARG cc_start: 0.8299 (tpt-90) cc_final: 0.7630 (tpp80) REVERT: F 52 GLU cc_start: 0.7977 (tp30) cc_final: 0.7604 (tp30) REVERT: F 91 LYS cc_start: 0.8625 (tttp) cc_final: 0.8173 (ttmt) REVERT: F 93 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: G 36 LYS cc_start: 0.9241 (mmpt) cc_final: 0.8694 (mmmm) REVERT: G 38 ASN cc_start: 0.8518 (t0) cc_final: 0.8113 (t0) REVERT: G 61 GLU cc_start: 0.8452 (tp30) cc_final: 0.8201 (tp30) REVERT: G 75 LYS cc_start: 0.7922 (mttt) cc_final: 0.7625 (mttp) REVERT: G 76 THR cc_start: 0.9055 (p) cc_final: 0.8803 (t) REVERT: G 83 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8266 (mp) REVERT: H 67 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8609 (t0) REVERT: H 68 ASP cc_start: 0.8073 (t70) cc_final: 0.7393 (t0) REVERT: H 86 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7543 (mtp180) REVERT: H 93 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7536 (tt0) REVERT: K 534 LYS cc_start: 0.4478 (pptt) cc_final: 0.4250 (tmmt) REVERT: M 1 MET cc_start: 0.2401 (ptt) cc_final: 0.1416 (ptp) REVERT: M 137 TRP cc_start: 0.7051 (m100) cc_final: 0.6832 (m100) REVERT: M 148 LYS cc_start: 0.8451 (mttt) cc_final: 0.8226 (mttt) REVERT: N 1 MET cc_start: -0.0120 (ptt) cc_final: -0.0576 (mtm) REVERT: N 77 HIS cc_start: 0.6923 (m90) cc_final: 0.6542 (m170) REVERT: N 78 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5909 (pm20) REVERT: N 137 TRP cc_start: 0.8437 (m100) cc_final: 0.7845 (m100) outliers start: 42 outliers final: 29 residues processed: 249 average time/residue: 0.1470 time to fit residues: 50.6060 Evaluate side-chains 241 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 67 ASN 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 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 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE 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 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN D 47 GLN H 67 ASN M 146 GLN N 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.180353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116184 restraints weight = 24745.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117999 restraints weight = 13181.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119988 restraints weight = 8305.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120117 restraints weight = 7573.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120079 restraints weight = 6896.502| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16702 Z= 0.152 Angle : 0.602 11.962 23819 Z= 0.346 Chirality : 0.036 0.160 2690 Planarity : 0.004 0.060 1986 Dihedral : 29.444 171.914 4651 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.52 % Allowed : 20.74 % Favored : 75.73 % 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: -2.68 (0.23), residues: 1196 helix: -1.14 (0.19), residues: 673 sheet: -1.41 (0.69), residues: 64 loop : -2.71 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.022 0.001 TYR H 83 PHE 0.014 0.001 PHE M 8 TRP 0.023 0.002 TRP M 28 HIS 0.002 0.000 HIS M 77 Details of bonding type rmsd covalent geometry : bond 0.00334 (16702) covalent geometry : angle 0.60234 (23819) hydrogen bonds : bond 0.04788 ( 478) hydrogen bonds : angle 3.86010 ( 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 262 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8484 (ttt180) REVERT: B 44 LYS cc_start: 0.8360 (tttt) cc_final: 0.8156 (tmtt) REVERT: B 68 ASP cc_start: 0.8538 (m-30) cc_final: 0.8236 (m-30) REVERT: B 91 LYS cc_start: 0.8796 (tttm) cc_final: 0.8403 (ttpt) REVERT: B 92 ARG cc_start: 0.9238 (ttp80) cc_final: 0.8482 (ttp80) REVERT: C 24 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8338 (mm-40) REVERT: C 36 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8129 (tmtt) REVERT: C 38 ASN cc_start: 0.8725 (t0) cc_final: 0.7155 (t0) REVERT: C 73 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7545 (t0) REVERT: C 95 LYS cc_start: 0.8971 (tptp) cc_final: 0.8348 (ttmt) REVERT: D 37 TYR cc_start: 0.8925 (m-80) cc_final: 0.8662 (m-80) REVERT: D 68 ASP cc_start: 0.8514 (t70) cc_final: 0.7951 (t0) REVERT: D 85 LYS cc_start: 0.8722 (mttt) cc_final: 0.8470 (mmtp) REVERT: F 52 GLU cc_start: 0.7806 (tp30) cc_final: 0.7418 (tp30) REVERT: F 91 LYS cc_start: 0.8582 (tttp) cc_final: 0.8091 (ttmt) REVERT: G 36 LYS cc_start: 0.9108 (mmpt) cc_final: 0.8656 (mmmm) REVERT: G 61 GLU cc_start: 0.8307 (tp30) cc_final: 0.8061 (tp30) REVERT: G 95 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8456 (mtpp) REVERT: H 68 ASP cc_start: 0.8034 (t70) cc_final: 0.7307 (t0) REVERT: H 86 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7313 (mtp180) REVERT: K 534 LYS cc_start: 0.4386 (pptt) cc_final: 0.4179 (tmmt) REVERT: M 1 MET cc_start: 0.2429 (ptt) cc_final: 0.1577 (ptp) REVERT: M 148 LYS cc_start: 0.8493 (mttt) cc_final: 0.8190 (mttt) REVERT: N 1 MET cc_start: -0.0122 (ptt) cc_final: -0.0723 (mtm) REVERT: N 77 HIS cc_start: 0.6889 (m90) cc_final: 0.6590 (m170) REVERT: N 78 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5833 (pm20) REVERT: N 137 TRP cc_start: 0.8401 (m100) cc_final: 0.7839 (m100) outliers start: 36 outliers final: 24 residues processed: 250 average time/residue: 0.1433 time to fit residues: 49.7380 Evaluate side-chains 243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 136 GLU 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 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 38 ASN C 73 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111453 restraints weight = 24568.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114693 restraints weight = 12265.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116622 restraints weight = 8590.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117546 restraints weight = 7285.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117932 restraints weight = 6783.446| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16702 Z= 0.202 Angle : 0.627 10.746 23819 Z= 0.357 Chirality : 0.038 0.185 2690 Planarity : 0.004 0.063 1986 Dihedral : 29.547 170.371 4648 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.91 % Allowed : 21.14 % Favored : 74.95 % 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: -1.02 (0.19), residues: 681 sheet: -1.19 (0.71), residues: 64 loop : -2.76 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 134 TYR 0.035 0.002 TYR H 83 PHE 0.010 0.001 PHE G 25 TRP 0.024 0.002 TRP M 137 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (16702) covalent geometry : angle 0.62674 (23819) hydrogen bonds : bond 0.04839 ( 478) hydrogen bonds : angle 3.97594 ( 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 261 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8307 (ttt-90) REVERT: B 68 ASP cc_start: 0.8538 (m-30) cc_final: 0.8163 (m-30) REVERT: B 91 LYS cc_start: 0.8772 (tttm) cc_final: 0.8378 (ttpt) REVERT: B 92 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8424 (ttp80) REVERT: C 24 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8299 (mm-40) REVERT: C 36 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8157 (tmtt) REVERT: C 38 ASN cc_start: 0.8656 (t0) cc_final: 0.8021 (t0) REVERT: C 73 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7694 (t0) REVERT: C 95 LYS cc_start: 0.8995 (tptp) cc_final: 0.8417 (ttmt) REVERT: D 37 TYR cc_start: 0.9012 (m-80) cc_final: 0.8615 (m-80) REVERT: D 68 ASP cc_start: 0.8611 (t70) cc_final: 0.8058 (t0) REVERT: D 85 LYS cc_start: 0.8780 (mttt) cc_final: 0.8528 (mmtp) REVERT: F 52 GLU cc_start: 0.7915 (tp30) cc_final: 0.7510 (tp30) REVERT: F 91 LYS cc_start: 0.8623 (tttp) cc_final: 0.8188 (ttmt) REVERT: F 93 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: G 36 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8679 (mmmm) REVERT: G 38 ASN cc_start: 0.8313 (t0) cc_final: 0.7902 (t0) REVERT: G 61 GLU cc_start: 0.8374 (tp30) cc_final: 0.8116 (tp30) REVERT: H 68 ASP cc_start: 0.8124 (t70) cc_final: 0.7368 (t0) REVERT: H 86 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7541 (mtp180) REVERT: K 525 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7352 (mtm-85) REVERT: K 529 ASP cc_start: 0.7563 (t0) cc_final: 0.7069 (t0) REVERT: K 534 LYS cc_start: 0.4777 (pptt) cc_final: 0.4351 (mmmt) REVERT: M 1 MET cc_start: 0.2445 (ptt) cc_final: 0.1554 (ptp) REVERT: M 40 ASN cc_start: 0.7800 (t0) cc_final: 0.7353 (t0) REVERT: M 137 TRP cc_start: 0.6894 (m100) cc_final: 0.6633 (m100) REVERT: M 148 LYS cc_start: 0.8468 (mttt) cc_final: 0.8030 (mttm) REVERT: N 1 MET cc_start: 0.0281 (ptt) cc_final: -0.0106 (mtm) REVERT: N 77 HIS cc_start: 0.7063 (m90) cc_final: 0.6729 (m170) REVERT: N 78 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5856 (pm20) outliers start: 40 outliers final: 28 residues processed: 246 average time/residue: 0.1462 time to fit residues: 50.1117 Evaluate side-chains 248 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 132 ILE 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 F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU 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 M residue 24 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 117 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 144 optimal weight: 0.0970 chunk 81 optimal weight: 7.9990 overall best weight: 2.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN D 47 GLN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.178759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112544 restraints weight = 24830.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115866 restraints weight = 12134.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117865 restraints weight = 8401.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118761 restraints weight = 7074.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119359 restraints weight = 6582.710| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16702 Z= 0.191 Angle : 0.622 11.780 23819 Z= 0.355 Chirality : 0.037 0.188 2690 Planarity : 0.004 0.064 1986 Dihedral : 29.485 170.280 4648 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.72 % Allowed : 21.14 % Favored : 75.15 % 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: -2.34 (0.23), residues: 1196 helix: -0.86 (0.19), residues: 683 sheet: -1.11 (0.72), residues: 64 loop : -2.61 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 134 TYR 0.013 0.001 TYR F 88 PHE 0.014 0.001 PHE M 8 TRP 0.014 0.002 TRP M 137 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00429 (16702) covalent geometry : angle 0.62224 (23819) hydrogen bonds : bond 0.04698 ( 478) hydrogen bonds : angle 3.91242 ( 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 261 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (ttt180) REVERT: B 68 ASP cc_start: 0.8538 (m-30) cc_final: 0.8092 (m-30) REVERT: B 84 MET cc_start: 0.7893 (tpp) cc_final: 0.7638 (mmt) REVERT: B 91 LYS cc_start: 0.8767 (tttm) cc_final: 0.8366 (ttpt) REVERT: B 92 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8429 (ttp80) REVERT: C 36 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8166 (tmtt) REVERT: C 38 ASN cc_start: 0.8628 (t0) cc_final: 0.8023 (t0) REVERT: C 73 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7577 (t0) REVERT: C 95 LYS cc_start: 0.8989 (tptp) cc_final: 0.8379 (ttmt) REVERT: D 37 TYR cc_start: 0.8993 (m-80) cc_final: 0.8651 (m-80) REVERT: D 68 ASP cc_start: 0.8626 (t70) cc_final: 0.8075 (t0) REVERT: D 85 LYS cc_start: 0.8761 (mttt) cc_final: 0.8513 (mmtp) REVERT: F 52 GLU cc_start: 0.7912 (tp30) cc_final: 0.7488 (tp30) REVERT: F 91 LYS cc_start: 0.8639 (tttp) cc_final: 0.8172 (ttmt) REVERT: F 93 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: G 38 ASN cc_start: 0.8338 (t0) cc_final: 0.7914 (t0) REVERT: G 61 GLU cc_start: 0.8356 (tp30) cc_final: 0.8100 (tp30) REVERT: H 68 ASP cc_start: 0.8112 (t70) cc_final: 0.7341 (t0) REVERT: H 86 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7421 (mtp180) REVERT: H 120 LYS cc_start: 0.7484 (tptt) cc_final: 0.7197 (tttp) REVERT: K 529 ASP cc_start: 0.7624 (t0) cc_final: 0.7135 (t0) REVERT: K 534 LYS cc_start: 0.4672 (pptt) cc_final: 0.4330 (mmmt) REVERT: L 522 ARG cc_start: 0.8729 (ptt90) cc_final: 0.8458 (ptt90) REVERT: M 1 MET cc_start: 0.2439 (ptt) cc_final: 0.1553 (ptp) REVERT: M 40 ASN cc_start: 0.7651 (t0) cc_final: 0.7162 (t0) REVERT: M 148 LYS cc_start: 0.8580 (mttt) cc_final: 0.8059 (mttm) REVERT: M 169 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.4994 (mpp80) REVERT: N 1 MET cc_start: 0.0152 (ptt) cc_final: -0.0454 (mtm) REVERT: N 77 HIS cc_start: 0.7116 (m90) cc_final: 0.6798 (m170) REVERT: N 78 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.5928 (pm20) REVERT: N 137 TRP cc_start: 0.8282 (m100) cc_final: 0.7745 (m100) outliers start: 38 outliers final: 27 residues processed: 245 average time/residue: 0.1477 time to fit residues: 50.2696 Evaluate side-chains 250 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 ILE 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 F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 67 ASN 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 M residue 24 ILE Chi-restraints excluded: chain M residue 169 ARG Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111426 restraints weight = 24660.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114694 restraints weight = 12088.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116673 restraints weight = 8400.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117546 restraints weight = 7085.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118164 restraints weight = 6597.113| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16702 Z= 0.204 Angle : 0.634 12.314 23819 Z= 0.359 Chirality : 0.038 0.189 2690 Planarity : 0.004 0.065 1986 Dihedral : 29.474 170.707 4648 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.62 % Allowed : 21.33 % Favored : 75.05 % 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: -2.25 (0.24), residues: 1196 helix: -0.77 (0.20), residues: 681 sheet: -1.15 (0.72), residues: 64 loop : -2.60 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 134 TYR 0.013 0.002 TYR B 88 PHE 0.013 0.001 PHE B 100 TRP 0.025 0.002 TRP M 137 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (16702) covalent geometry : angle 0.63409 (23819) hydrogen bonds : bond 0.04750 ( 478) hydrogen bonds : angle 3.93542 ( 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 261 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8510 (ttt180) REVERT: B 68 ASP cc_start: 0.8568 (m-30) cc_final: 0.8134 (m-30) REVERT: B 88 TYR cc_start: 0.8137 (m-80) cc_final: 0.7842 (m-80) REVERT: B 91 LYS cc_start: 0.8712 (tttm) cc_final: 0.8298 (ttpt) REVERT: B 92 ARG cc_start: 0.9242 (ttp80) cc_final: 0.8441 (ttp80) REVERT: C 36 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8185 (tmtt) REVERT: C 38 ASN cc_start: 0.8660 (t0) cc_final: 0.8047 (t0) REVERT: C 73 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7658 (t0) REVERT: C 95 LYS cc_start: 0.8991 (tptp) cc_final: 0.8392 (ttmt) REVERT: D 37 TYR cc_start: 0.9009 (m-80) cc_final: 0.8601 (m-80) REVERT: D 68 ASP cc_start: 0.8640 (t70) cc_final: 0.8095 (t0) REVERT: D 85 LYS cc_start: 0.8770 (mttt) cc_final: 0.8508 (mmtp) REVERT: F 52 GLU cc_start: 0.7955 (tp30) cc_final: 0.7505 (tp30) REVERT: F 91 LYS cc_start: 0.8624 (tttp) cc_final: 0.8132 (ttmt) REVERT: F 93 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: G 38 ASN cc_start: 0.8346 (t0) cc_final: 0.7911 (t0) REVERT: G 75 LYS cc_start: 0.7724 (mttt) cc_final: 0.7471 (mttp) REVERT: H 68 ASP cc_start: 0.8067 (t70) cc_final: 0.7354 (t0) REVERT: H 86 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7458 (mtp180) REVERT: H 120 LYS cc_start: 0.7550 (tptt) cc_final: 0.7264 (tttp) REVERT: K 525 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7503 (mtm-85) REVERT: K 529 ASP cc_start: 0.7798 (t0) cc_final: 0.7335 (t0) REVERT: K 534 LYS cc_start: 0.4820 (pptt) cc_final: 0.4499 (mmmt) REVERT: M 1 MET cc_start: 0.2383 (ptt) cc_final: 0.1484 (ptp) REVERT: M 169 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.5014 (mpp80) REVERT: N 1 MET cc_start: 0.0196 (ptt) cc_final: -0.0371 (mtm) REVERT: N 77 HIS cc_start: 0.7067 (m90) cc_final: 0.6747 (m170) REVERT: N 78 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: N 137 TRP cc_start: 0.8272 (m100) cc_final: 0.7730 (m100) outliers start: 37 outliers final: 30 residues processed: 249 average time/residue: 0.1485 time to fit residues: 50.6818 Evaluate side-chains 253 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 136 GLU 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 F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 67 ASN 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 M residue 24 ILE Chi-restraints excluded: chain M residue 169 ARG Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 20.0000 chunk 58 optimal weight: 0.0870 chunk 78 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.175265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108556 restraints weight = 24762.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111576 restraints weight = 12777.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113377 restraints weight = 9100.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114208 restraints weight = 7763.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114578 restraints weight = 7254.093| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16702 Z= 0.306 Angle : 0.722 12.084 23819 Z= 0.401 Chirality : 0.042 0.195 2690 Planarity : 0.005 0.074 1986 Dihedral : 29.683 174.395 4648 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.62 % Favored : 89.30 % Rotamer: Outliers : 3.72 % Allowed : 22.02 % Favored : 74.27 % 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: -2.47 (0.23), residues: 1196 helix: -1.01 (0.19), residues: 685 sheet: -1.38 (0.67), residues: 70 loop : -2.57 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 55 TYR 0.021 0.002 TYR H 83 PHE 0.018 0.002 PHE C 25 TRP 0.022 0.002 TRP M 137 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00701 (16702) covalent geometry : angle 0.72151 (23819) hydrogen bonds : bond 0.05382 ( 478) hydrogen bonds : angle 4.36964 ( 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 258 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8437 (ttt-90) REVERT: B 91 LYS cc_start: 0.8707 (tttm) cc_final: 0.8336 (ttpt) REVERT: B 92 ARG cc_start: 0.9236 (ttp80) cc_final: 0.8564 (ttp80) REVERT: C 36 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8241 (tmtt) REVERT: C 38 ASN cc_start: 0.8640 (t0) cc_final: 0.8108 (t0) REVERT: C 73 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7545 (t0) REVERT: C 95 LYS cc_start: 0.9030 (tptp) cc_final: 0.8416 (ttmt) REVERT: D 68 ASP cc_start: 0.8694 (t70) cc_final: 0.8172 (t0) REVERT: F 52 GLU cc_start: 0.7979 (tp30) cc_final: 0.7541 (tp30) REVERT: F 91 LYS cc_start: 0.8627 (tttp) cc_final: 0.8209 (ttmt) REVERT: F 93 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: G 38 ASN cc_start: 0.8181 (t0) cc_final: 0.7856 (t0) REVERT: G 75 LYS cc_start: 0.7853 (mttt) cc_final: 0.7579 (mttp) REVERT: H 68 ASP cc_start: 0.8081 (t70) cc_final: 0.7411 (t0) REVERT: H 86 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7581 (mtp180) REVERT: H 120 LYS cc_start: 0.7626 (tptt) cc_final: 0.7335 (tttp) REVERT: K 529 ASP cc_start: 0.7973 (t0) cc_final: 0.7639 (t0) REVERT: K 534 LYS cc_start: 0.5037 (pptt) cc_final: 0.4813 (mmmt) REVERT: M 1 MET cc_start: 0.2295 (ptt) cc_final: 0.1404 (ptp) REVERT: M 137 TRP cc_start: 0.6921 (m100) cc_final: 0.6159 (m100) REVERT: N 77 HIS cc_start: 0.7114 (m90) cc_final: 0.6806 (m170) REVERT: N 78 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5843 (pm20) REVERT: N 137 TRP cc_start: 0.8344 (m100) cc_final: 0.7768 (m100) REVERT: N 151 TYR cc_start: 0.8301 (m-80) cc_final: 0.8062 (m-10) outliers start: 38 outliers final: 30 residues processed: 244 average time/residue: 0.1473 time to fit residues: 49.5592 Evaluate side-chains 246 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 A residue 113 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 ILE 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 F residue 93 GLN Chi-restraints excluded: chain G residue 65 LEU 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 M residue 24 ILE Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 131 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.175925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109558 restraints weight = 24765.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112597 restraints weight = 12654.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114303 restraints weight = 8979.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115340 restraints weight = 7681.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115755 restraints weight = 7129.369| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 16702 Z= 0.270 Angle : 0.901 59.196 23819 Z= 0.525 Chirality : 0.044 1.003 2690 Planarity : 0.006 0.133 1986 Dihedral : 29.691 174.203 4648 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.62 % Favored : 89.21 % Rotamer: Outliers : 3.62 % Allowed : 22.11 % Favored : 74.27 % Cbeta Deviations : 0.09 % 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: -2.46 (0.23), residues: 1196 helix: -0.99 (0.19), residues: 684 sheet: -1.37 (0.67), residues: 70 loop : -2.59 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 134 TYR 0.026 0.002 TYR B 88 PHE 0.016 0.002 PHE C 25 TRP 0.017 0.002 TRP M 137 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00629 (16702) covalent geometry : angle 0.90103 (23819) hydrogen bonds : bond 0.05284 ( 478) hydrogen bonds : angle 4.33890 ( 1273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.07 seconds wall clock time: 50 minutes 27.23 seconds (3027.23 seconds total)