Starting phenix.real_space_refine on Sat Mar 7 10:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.map" model { file = "/net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w7n_21572/03_2026/6w7n_21572.cif" } resolution = 3.4 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= -0.000 sd= 0.992 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 1372 5.49 5 S 38 5.16 5 C 21145 2.51 5 N 7915 2.21 5 O 11817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s 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: 42287 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 29443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1372, 29443 Classifications: {'RNA': 1372} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 68, 'rna3p_pur': 680, 'rna3p_pyr': 521} Link IDs: {'rna2p': 171, 'rna3p': 1200} Chain breaks: 3 Chain: "C" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1622 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1602 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1073 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 144} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 958 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 903 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 610 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 77} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 638 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.94, per 1000 atoms: 0.21 Number of scatterers: 42287 At special positions: 0 Unit cell: (206.016, 221.038, 157.731, 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 38 16.00 P 1372 15.00 O 11817 8.00 N 7915 7.00 C 21145 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: 3.35 Conformation dependent library (CDL) restraints added in 899.7 milliseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 37.8% alpha, 13.8% beta 352 base pairs and 708 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.808A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.514A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.187A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.093A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.836A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.780A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.615A pdb=" N ASN D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.640A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.588A pdb=" N GLN D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.695A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.937A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 68 removed outlier: 3.926A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 115 removed outlier: 3.504A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.761A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 93 through 98 removed outlier: 3.945A pdb=" N ALA H 96 " --> pdb=" O LYS H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.823A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.869A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 100 Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.573A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 88 removed outlier: 3.581A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 88' Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.526A pdb=" N SER M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 56 removed outlier: 4.442A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 61 removed outlier: 3.706A pdb=" N ALA M 60 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS M 61 " --> pdb=" O GLU M 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 57 through 61' Processing helix chain 'M' and resid 65 through 81 Processing helix chain 'M' and resid 84 through 92 removed outlier: 4.115A pdb=" N ARG M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.647A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 18 removed outlier: 3.522A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 removed outlier: 3.710A pdb=" N ARG N 23 " --> pdb=" O TYR N 19 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 49 removed outlier: 4.083A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 Processing helix chain 'O' and resid 3 through 14 removed outlier: 3.663A pdb=" N SER O 12 " --> pdb=" O ALA O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.754A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 71 removed outlier: 3.547A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 80 removed outlier: 3.522A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.787A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 3.504A pdb=" N ALA P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.647A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 Processing helix chain 'S' and resid 70 through 74 Processing helix chain 'T' and resid 5 through 38 removed outlier: 3.838A pdb=" N ARG T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 51 Processing helix chain 'T' and resid 53 through 61 removed outlier: 3.639A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 83 removed outlier: 3.963A pdb=" N GLN T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.589A pdb=" N THR C 20 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 152 Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 173 removed outlier: 3.624A pdb=" N THR D 180 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 16 removed outlier: 7.015A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AA7, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.570A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 76 removed outlier: 6.945A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.592A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AB6, first strand: chain 'L' and resid 35 through 37 removed outlier: 3.539A pdb=" N TYR L 37 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL L 51 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 64 " --> pdb=" O CYS L 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 54 " --> pdb=" O VAL L 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 20 through 21 removed outlier: 3.715A pdb=" N GLU P 34 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 7 through 13 removed outlier: 7.329A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS Q 63 " --> pdb=" O SER Q 71 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 30 through 32 removed outlier: 3.667A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL S 50 " --> pdb=" O VAL S 57 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 897 hydrogen bonds 1462 hydrogen bond angles 0 basepair planarities 352 basepair parallelities 708 stacking parallelities Total time for adding SS restraints: 15.03 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5869 1.33 - 1.45: 19042 1.45 - 1.57: 18265 1.57 - 1.69: 2740 1.69 - 1.81: 69 Bond restraints: 45985 Sorted by residual: bond pdb=" C ILE J 53 " pdb=" N SER J 54 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.59e-02 3.96e+03 2.18e+00 bond pdb=" C LEU J 42 " pdb=" N PRO J 43 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.27e-02 6.20e+03 2.03e+00 bond pdb=" N LEU L 48 " pdb=" CA LEU L 48 " ideal model delta sigma weight residual 1.468 1.451 0.017 1.24e-02 6.50e+03 1.85e+00 bond pdb=" O5' A A 923 " pdb=" C5' A A 923 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.75e+00 bond pdb=" O5' G A 922 " pdb=" C5' G A 922 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.68e+00 ... (remaining 45980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 67911 1.54 - 3.09: 839 3.09 - 4.63: 121 4.63 - 6.18: 33 6.18 - 7.72: 6 Bond angle restraints: 68910 Sorted by residual: angle pdb=" C3' A A1201 " pdb=" O3' A A1201 " pdb=" P U A1202 " ideal model delta sigma weight residual 120.20 125.66 -5.46 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C3' G A1300 " pdb=" O3' G A1300 " pdb=" P U A1301 " ideal model delta sigma weight residual 120.20 125.58 -5.38 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C LEU L 48 " pdb=" N ARG L 49 " pdb=" CA ARG L 49 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C3' A A 60 " pdb=" O3' A A 60 " pdb=" P G A 61 " ideal model delta sigma weight residual 120.20 125.51 -5.31 1.50e+00 4.44e-01 1.25e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 120.20 125.51 -5.31 1.50e+00 4.44e-01 1.25e+01 ... (remaining 68905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 26014 35.67 - 71.34: 3090 71.34 - 107.01: 388 107.01 - 142.67: 3 142.67 - 178.34: 11 Dihedral angle restraints: 29506 sinusoidal: 24759 harmonic: 4747 Sorted by residual: dihedral pdb=" CA VAL J 57 " pdb=" C VAL J 57 " pdb=" N ASN J 58 " pdb=" CA ASN J 58 " ideal model delta harmonic sigma weight residual -180.00 -123.63 -56.37 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual 200.00 39.95 160.05 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 46.16 153.84 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 29503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8065 0.045 - 0.091: 609 0.091 - 0.136: 126 0.136 - 0.181: 19 0.181 - 0.226: 8 Chirality restraints: 8827 Sorted by residual: chirality pdb=" C3' U A1528 " pdb=" C4' U A1528 " pdb=" O3' U A1528 " pdb=" C2' U A1528 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' G A 484 " pdb=" C4' G A 484 " pdb=" O3' G A 484 " pdb=" C2' G A 484 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' A A 60 " pdb=" C4' A A 60 " pdb=" O3' A A 60 " pdb=" C2' A A 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 8824 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 363 " 0.033 2.00e-02 2.50e+03 1.47e-02 5.98e+00 pdb=" N9 A A 363 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A A 363 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A 363 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A 363 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 363 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 363 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A A 363 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A 363 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 363 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A A 363 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 504 " -0.021 2.00e-02 2.50e+03 1.53e-02 5.29e+00 pdb=" N1 C A 504 " 0.017 2.00e-02 2.50e+03 pdb=" C2 C A 504 " 0.032 2.00e-02 2.50e+03 pdb=" O2 C A 504 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C A 504 " -0.018 2.00e-02 2.50e+03 pdb=" C4 C A 504 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C A 504 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C A 504 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 504 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1141 " -0.002 2.00e-02 2.50e+03 1.52e-02 5.23e+00 pdb=" N1 C A1141 " -0.000 2.00e-02 2.50e+03 pdb=" C2 C A1141 " 0.038 2.00e-02 2.50e+03 pdb=" O2 C A1141 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A1141 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A1141 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C A1141 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A1141 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A1141 " -0.002 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 208 2.51 - 3.10: 28054 3.10 - 3.70: 76188 3.70 - 4.30: 109112 4.30 - 4.90: 151146 Nonbonded interactions: 364708 Sorted by model distance: nonbonded pdb=" O2 U A 17 " pdb=" N2 G A1079 " model vdw 1.907 3.120 nonbonded pdb=" OP1 G A1074 " pdb=" NH2 ARG E 68 " model vdw 2.011 3.120 nonbonded pdb=" O2' G A1124 " pdb=" O6 G A1127 " model vdw 2.149 3.040 nonbonded pdb=" OP1 G A 126 " pdb=" O2' U A 605 " model vdw 2.153 3.040 nonbonded pdb=" O2 U A 672 " pdb=" O6 G A 734 " model vdw 2.195 2.432 ... (remaining 364703 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 45.950 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.002 0.036 45985 Z= 0.104 Angle : 0.461 7.720 68910 Z= 0.252 Chirality : 0.027 0.226 8827 Planarity : 0.003 0.035 3644 Dihedral : 22.814 178.344 26440 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.16 % Favored : 91.53 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.03 (0.18), residues: 1630 helix: -1.84 (0.20), residues: 563 sheet: -2.76 (0.28), residues: 274 loop : -3.30 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 2 TYR 0.007 0.001 TYR M 85 PHE 0.008 0.001 PHE M 62 TRP 0.004 0.001 TRP P 60 HIS 0.007 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00185 (45985) covalent geometry : angle 0.46145 (68910) hydrogen bonds : bond 0.12753 ( 1361) hydrogen bonds : angle 4.83704 ( 2794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.7448 (tppt) cc_final: 0.6750 (pttt) REVERT: C 166 TRP cc_start: 0.5535 (t-100) cc_final: 0.5183 (t-100) REVERT: D 122 ILE cc_start: 0.9060 (mp) cc_final: 0.8859 (mp) REVERT: D 130 ASN cc_start: 0.9031 (p0) cc_final: 0.8665 (p0) REVERT: D 173 ASP cc_start: 0.7676 (t0) cc_final: 0.7343 (t0) REVERT: E 12 GLU cc_start: 0.7293 (pt0) cc_final: 0.7041 (pt0) REVERT: E 85 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8142 (tttm) REVERT: H 117 GLN cc_start: 0.8258 (tt0) cc_final: 0.7940 (mt0) REVERT: I 78 ILE cc_start: 0.6061 (mm) cc_final: 0.5651 (mm) REVERT: J 31 ARG cc_start: 0.5488 (tpp80) cc_final: 0.4588 (ptp-110) REVERT: N 11 LYS cc_start: 0.6937 (ptmm) cc_final: 0.6393 (mtmt) REVERT: O 48 ASP cc_start: 0.8287 (t0) cc_final: 0.7553 (t70) REVERT: O 70 LYS cc_start: 0.8154 (tppp) cc_final: 0.7364 (tmmt) REVERT: P 76 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8163 (mmtt) REVERT: Q 80 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7736 (mmmm) REVERT: T 52 GLU cc_start: 0.7815 (pp20) cc_final: 0.7507 (pp20) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.3279 time to fit residues: 157.6450 Evaluate side-chains 214 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0370 chunk 111 optimal weight: 20.0000 overall best weight: 5.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 18 ASN C 40 GLN C 68 HIS C 175 HIS D 39 GLN E 82 HIS E 147 ASN H 3 GLN I 30 ASN I 31 GLN J 35 GLN L 4 ASN L 45 ASN L 95 HIS N 3 GLN N 48 GLN O 34 GLN P 26 ASN S 42 ASN S 56 HIS ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.147947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113758 restraints weight = 93221.138| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.08 r_work: 0.3166 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 45985 Z= 0.324 Angle : 0.709 9.051 68910 Z= 0.355 Chirality : 0.037 0.304 8827 Planarity : 0.005 0.067 3644 Dihedral : 23.365 178.384 23289 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.86 % Favored : 88.90 % Rotamer: Outliers : 3.29 % Allowed : 14.32 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.54 (0.19), residues: 1630 helix: -1.33 (0.20), residues: 571 sheet: -2.76 (0.28), residues: 297 loop : -2.97 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 80 TYR 0.022 0.002 TYR D 50 PHE 0.023 0.002 PHE S 73 TRP 0.014 0.002 TRP C 200 HIS 0.007 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00635 (45985) covalent geometry : angle 0.70863 (68910) hydrogen bonds : bond 0.07619 ( 1361) hydrogen bonds : angle 3.64855 ( 2794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 GLU cc_start: 0.8329 (tp30) cc_final: 0.8078 (tp30) REVERT: E 85 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8382 (tttm) REVERT: H 117 GLN cc_start: 0.8716 (tt0) cc_final: 0.8266 (mt0) REVERT: I 118 ARG cc_start: 0.6689 (mtm110) cc_final: 0.5623 (ttt90) REVERT: J 31 ARG cc_start: 0.5436 (tpp80) cc_final: 0.4852 (ptp-110) REVERT: M 70 ARG cc_start: 0.5554 (mmp-170) cc_final: 0.4331 (mmt180) REVERT: M 78 ARG cc_start: 0.5734 (ptt90) cc_final: 0.4982 (pmt-80) REVERT: N 11 LYS cc_start: 0.7029 (ptmm) cc_final: 0.6552 (mtmt) REVERT: N 41 TRP cc_start: 0.5752 (p90) cc_final: 0.4870 (m-10) REVERT: O 48 ASP cc_start: 0.8409 (t0) cc_final: 0.8023 (t70) REVERT: P 76 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8530 (mmtt) REVERT: Q 80 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7594 (tptm) REVERT: S 33 TRP cc_start: 0.7768 (m100) cc_final: 0.6794 (m-10) REVERT: T 52 GLU cc_start: 0.8280 (pp20) cc_final: 0.7735 (pp20) outliers start: 43 outliers final: 34 residues processed: 251 average time/residue: 0.2852 time to fit residues: 112.8633 Evaluate side-chains 234 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 58 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS E 60 GLN H 75 GLN L 95 HIS N 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.149705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.114744 restraints weight = 93402.594| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.17 r_work: 0.3193 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 45985 Z= 0.173 Angle : 0.551 9.405 68910 Z= 0.283 Chirality : 0.032 0.253 8827 Planarity : 0.004 0.051 3644 Dihedral : 23.258 178.704 23289 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.02 % Favored : 90.74 % Rotamer: Outliers : 3.06 % Allowed : 18.15 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.97 (0.19), residues: 1630 helix: -0.76 (0.21), residues: 575 sheet: -2.33 (0.29), residues: 289 loop : -2.79 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 86 TYR 0.014 0.001 TYR D 3 PHE 0.010 0.001 PHE P 32 TRP 0.008 0.001 TRP C 200 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00337 (45985) covalent geometry : angle 0.55095 (68910) hydrogen bonds : bond 0.05807 ( 1361) hydrogen bonds : angle 3.30089 ( 2794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6989 (m-80) cc_final: 0.6598 (m-80) REVERT: C 165 GLU cc_start: 0.8336 (tp30) cc_final: 0.8041 (tp30) REVERT: E 71 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8035 (tt) REVERT: E 85 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8355 (tttm) REVERT: H 117 GLN cc_start: 0.8737 (tt0) cc_final: 0.8315 (mt0) REVERT: I 114 LYS cc_start: 0.8729 (mppt) cc_final: 0.8321 (mptt) REVERT: I 118 ARG cc_start: 0.6688 (mtm110) cc_final: 0.5812 (ttt90) REVERT: J 31 ARG cc_start: 0.5495 (tpp80) cc_final: 0.4882 (ptp-110) REVERT: L 49 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6535 (mmp-170) REVERT: L 88 ASP cc_start: 0.7624 (m-30) cc_final: 0.7421 (m-30) REVERT: M 86 ARG cc_start: 0.3549 (tpt90) cc_final: 0.2618 (tpt-90) REVERT: M 89 ARG cc_start: 0.1359 (mmt180) cc_final: 0.1083 (mmt-90) REVERT: N 11 LYS cc_start: 0.7013 (ptmm) cc_final: 0.6518 (mtmt) REVERT: O 44 GLU cc_start: 0.6914 (mp0) cc_final: 0.6199 (mp0) REVERT: O 48 ASP cc_start: 0.8282 (t0) cc_final: 0.7933 (t70) REVERT: O 70 LYS cc_start: 0.8626 (tppp) cc_final: 0.7751 (tmtt) REVERT: P 53 ASP cc_start: 0.8781 (t0) cc_final: 0.8515 (t0) REVERT: P 76 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8489 (mmtm) REVERT: Q 80 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7583 (tptm) REVERT: T 52 GLU cc_start: 0.8243 (pp20) cc_final: 0.7692 (pp20) outliers start: 40 outliers final: 25 residues processed: 241 average time/residue: 0.2999 time to fit residues: 112.8931 Evaluate side-chains 235 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 103 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 277 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 40.0000 chunk 221 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS M 90 HIS N 59 GLN N 70 HIS O 45 HIS ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.145889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111512 restraints weight = 92598.517| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.43 r_work: 0.3132 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 45985 Z= 0.342 Angle : 0.725 9.491 68910 Z= 0.364 Chirality : 0.039 0.305 8827 Planarity : 0.005 0.064 3644 Dihedral : 23.431 178.986 23289 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.10 % Favored : 88.59 % Rotamer: Outliers : 4.67 % Allowed : 18.45 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.07 (0.19), residues: 1630 helix: -0.86 (0.21), residues: 573 sheet: -2.47 (0.28), residues: 305 loop : -2.78 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 79 TYR 0.019 0.002 TYR D 50 PHE 0.056 0.003 PHE I 102 TRP 0.012 0.002 TRP C 200 HIS 0.007 0.002 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00669 (45985) covalent geometry : angle 0.72529 (68910) hydrogen bonds : bond 0.07798 ( 1361) hydrogen bonds : angle 3.56900 ( 2794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7063 (m-80) cc_final: 0.6634 (m-80) REVERT: C 165 GLU cc_start: 0.8443 (tp30) cc_final: 0.8060 (tp30) REVERT: E 70 MET cc_start: 0.8210 (ttp) cc_final: 0.7999 (ttp) REVERT: E 71 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8063 (tt) REVERT: E 85 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8353 (tttm) REVERT: H 117 GLN cc_start: 0.8797 (tt0) cc_final: 0.8363 (mt0) REVERT: I 114 LYS cc_start: 0.8925 (mppt) cc_final: 0.8470 (mptt) REVERT: I 118 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6409 (ttt90) REVERT: J 31 ARG cc_start: 0.5567 (tpp80) cc_final: 0.4989 (ptp-110) REVERT: J 66 GLU cc_start: 0.8598 (pp20) cc_final: 0.7776 (pp20) REVERT: L 49 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6497 (mmp-170) REVERT: M 70 ARG cc_start: 0.5354 (mmp-170) cc_final: 0.4143 (mmt180) REVERT: M 78 ARG cc_start: 0.5576 (ptt90) cc_final: 0.4872 (pmt-80) REVERT: M 90 HIS cc_start: 0.5871 (OUTLIER) cc_final: 0.5585 (t70) REVERT: N 11 LYS cc_start: 0.7140 (ptmm) cc_final: 0.6636 (mtmt) REVERT: N 20 PHE cc_start: 0.4137 (OUTLIER) cc_final: 0.3594 (t80) REVERT: N 59 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6840 (mp-120) REVERT: O 48 ASP cc_start: 0.8374 (t0) cc_final: 0.8108 (t70) REVERT: P 53 ASP cc_start: 0.8799 (t0) cc_final: 0.8522 (t0) REVERT: P 76 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8606 (mmtt) REVERT: Q 80 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7663 (tptm) REVERT: T 52 GLU cc_start: 0.8349 (pp20) cc_final: 0.7692 (pp20) outliers start: 61 outliers final: 45 residues processed: 246 average time/residue: 0.2891 time to fit residues: 111.5610 Evaluate side-chains 234 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 292 optimal weight: 9.9990 chunk 198 optimal weight: 0.0470 chunk 146 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 204 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS E 60 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS N 59 GLN O 45 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.150384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115300 restraints weight = 93191.876| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.27 r_work: 0.3235 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45985 Z= 0.114 Angle : 0.524 9.240 68910 Z= 0.273 Chirality : 0.031 0.227 8827 Planarity : 0.004 0.072 3644 Dihedral : 23.256 178.708 23289 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.09 % Rotamer: Outliers : 3.22 % Allowed : 21.06 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1630 helix: -0.27 (0.22), residues: 570 sheet: -1.94 (0.31), residues: 276 loop : -2.61 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 28 TYR 0.015 0.001 TYR D 3 PHE 0.015 0.001 PHE M 62 TRP 0.015 0.001 TRP C 166 HIS 0.024 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00217 (45985) covalent geometry : angle 0.52396 (68910) hydrogen bonds : bond 0.05505 ( 1361) hydrogen bonds : angle 3.09786 ( 2794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7052 (m-80) cc_final: 0.6671 (m-80) REVERT: C 48 LYS cc_start: 0.7225 (tptt) cc_final: 0.6655 (tppt) REVERT: C 165 GLU cc_start: 0.8253 (tp30) cc_final: 0.7908 (tp30) REVERT: D 130 ASN cc_start: 0.8910 (p0) cc_final: 0.8623 (p0) REVERT: D 164 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7867 (mtm110) REVERT: E 71 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8016 (tt) REVERT: E 85 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8293 (tttm) REVERT: H 117 GLN cc_start: 0.8681 (tt0) cc_final: 0.8311 (mt0) REVERT: I 118 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6347 (ttt90) REVERT: J 31 ARG cc_start: 0.5562 (tpp80) cc_final: 0.4966 (ptp-110) REVERT: J 66 GLU cc_start: 0.8606 (pp20) cc_final: 0.7754 (pp20) REVERT: L 49 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6704 (mmp-170) REVERT: N 11 LYS cc_start: 0.7051 (ptmm) cc_final: 0.6556 (mtmt) REVERT: N 20 PHE cc_start: 0.3941 (OUTLIER) cc_final: 0.3576 (t80) REVERT: N 41 TRP cc_start: 0.6047 (p90) cc_final: 0.5236 (m-90) REVERT: N 59 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: O 48 ASP cc_start: 0.8158 (t0) cc_final: 0.7794 (t70) REVERT: O 70 LYS cc_start: 0.8595 (tppp) cc_final: 0.7926 (tmmt) REVERT: P 53 ASP cc_start: 0.8694 (t0) cc_final: 0.8468 (t0) REVERT: P 76 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8559 (mmtm) REVERT: Q 80 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7607 (tptm) REVERT: S 68 HIS cc_start: 0.4084 (OUTLIER) cc_final: 0.3535 (m-70) REVERT: T 52 GLU cc_start: 0.8219 (pp20) cc_final: 0.7611 (pp20) REVERT: T 54 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8197 (tm-30) outliers start: 42 outliers final: 24 residues processed: 246 average time/residue: 0.2809 time to fit residues: 108.9402 Evaluate side-chains 224 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 196 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 169 optimal weight: 0.0020 chunk 155 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 234 optimal weight: 0.0050 chunk 23 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 overall best weight: 3.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS N 59 GLN ** T 67 HIS ** 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 = 0.4170 r_free = 0.4170 target = 0.147740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.113494 restraints weight = 92372.134| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.08 r_work: 0.3180 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 45985 Z= 0.218 Angle : 0.590 9.278 68910 Z= 0.301 Chirality : 0.034 0.269 8827 Planarity : 0.005 0.108 3644 Dihedral : 23.238 178.129 23289 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.49 % Favored : 89.26 % Rotamer: Outliers : 4.13 % Allowed : 20.83 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.42 (0.20), residues: 1630 helix: -0.27 (0.22), residues: 570 sheet: -1.99 (0.30), residues: 303 loop : -2.50 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 52 TYR 0.013 0.002 TYR D 50 PHE 0.014 0.002 PHE M 62 TRP 0.010 0.002 TRP C 166 HIS 0.007 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00426 (45985) covalent geometry : angle 0.59042 (68910) hydrogen bonds : bond 0.06271 ( 1361) hydrogen bonds : angle 3.21326 ( 2794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7037 (m-80) cc_final: 0.6614 (m-80) REVERT: C 48 LYS cc_start: 0.7190 (tptt) cc_final: 0.6597 (tppt) REVERT: C 165 GLU cc_start: 0.8202 (tp30) cc_final: 0.7837 (tp30) REVERT: D 130 ASN cc_start: 0.8936 (p0) cc_final: 0.8610 (p0) REVERT: E 71 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (tt) REVERT: E 85 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8302 (tttm) REVERT: H 117 GLN cc_start: 0.8702 (tt0) cc_final: 0.8300 (mt0) REVERT: I 114 LYS cc_start: 0.8828 (mppt) cc_final: 0.8549 (mptt) REVERT: I 118 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6501 (ttt90) REVERT: J 31 ARG cc_start: 0.5363 (tpp80) cc_final: 0.4836 (ptp-110) REVERT: J 66 GLU cc_start: 0.8629 (pp20) cc_final: 0.7831 (pp20) REVERT: J 88 MET cc_start: 0.6743 (mmm) cc_final: 0.6289 (tmm) REVERT: L 49 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6650 (mmp-170) REVERT: N 11 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6500 (mtmt) REVERT: N 20 PHE cc_start: 0.3639 (OUTLIER) cc_final: 0.3247 (t80) REVERT: N 22 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5346 (pptt) REVERT: N 41 TRP cc_start: 0.5797 (p90) cc_final: 0.5123 (m-90) REVERT: N 59 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: N 91 GLU cc_start: 0.8022 (mt-10) cc_final: 0.6707 (mp0) REVERT: O 48 ASP cc_start: 0.8213 (t0) cc_final: 0.7770 (t70) REVERT: P 53 ASP cc_start: 0.8727 (t0) cc_final: 0.8457 (t0) REVERT: P 76 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8584 (mmtt) REVERT: Q 80 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7656 (tptm) REVERT: S 68 HIS cc_start: 0.4241 (OUTLIER) cc_final: 0.3656 (m-70) REVERT: T 52 GLU cc_start: 0.8314 (pp20) cc_final: 0.7675 (pp20) REVERT: T 54 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 54 outliers final: 34 residues processed: 225 average time/residue: 0.2763 time to fit residues: 99.2990 Evaluate side-chains 224 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 267 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 233 optimal weight: 0.0570 chunk 207 optimal weight: 0.2980 chunk 235 optimal weight: 0.0970 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS E 60 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.150941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116465 restraints weight = 92886.000| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.19 r_work: 0.3249 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 45985 Z= 0.106 Angle : 0.503 14.205 68910 Z= 0.259 Chirality : 0.030 0.219 8827 Planarity : 0.004 0.051 3644 Dihedral : 23.179 177.970 23289 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.04 % Favored : 91.72 % Rotamer: Outliers : 3.68 % Allowed : 21.29 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.04 (0.21), residues: 1630 helix: 0.15 (0.23), residues: 561 sheet: -1.73 (0.31), residues: 301 loop : -2.38 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 51 TYR 0.017 0.001 TYR D 3 PHE 0.015 0.001 PHE M 62 TRP 0.016 0.001 TRP C 166 HIS 0.005 0.001 HIS P 59 Details of bonding type rmsd covalent geometry : bond 0.00200 (45985) covalent geometry : angle 0.50303 (68910) hydrogen bonds : bond 0.05189 ( 1361) hydrogen bonds : angle 3.00730 ( 2794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6904 (m-80) cc_final: 0.6550 (m-80) REVERT: C 48 LYS cc_start: 0.7304 (tptt) cc_final: 0.6743 (tppt) REVERT: C 165 GLU cc_start: 0.8089 (tp30) cc_final: 0.7790 (tp30) REVERT: D 130 ASN cc_start: 0.8907 (p0) cc_final: 0.8651 (p0) REVERT: D 164 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7876 (mtm110) REVERT: E 71 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7905 (tt) REVERT: E 85 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8188 (tttm) REVERT: H 117 GLN cc_start: 0.8768 (tt0) cc_final: 0.8328 (mt0) REVERT: I 114 LYS cc_start: 0.8816 (mppt) cc_final: 0.8584 (mptt) REVERT: I 118 ARG cc_start: 0.7028 (mtm110) cc_final: 0.6433 (ttt90) REVERT: J 31 ARG cc_start: 0.5267 (tpp80) cc_final: 0.4783 (ptp-110) REVERT: J 88 MET cc_start: 0.6799 (mmm) cc_final: 0.6337 (mmm) REVERT: L 49 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6305 (mmp-170) REVERT: M 70 ARG cc_start: 0.5418 (mmp-170) cc_final: 0.4196 (mmt180) REVERT: N 5 MET cc_start: 0.4640 (ptp) cc_final: 0.4025 (ptp) REVERT: N 11 LYS cc_start: 0.7048 (ptmm) cc_final: 0.6548 (mtmt) REVERT: N 20 PHE cc_start: 0.3742 (OUTLIER) cc_final: 0.3411 (t80) REVERT: N 22 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5376 (pptt) REVERT: N 41 TRP cc_start: 0.5835 (p90) cc_final: 0.5210 (m-90) REVERT: N 47 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7508 (mt) REVERT: N 91 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6657 (mp0) REVERT: O 48 ASP cc_start: 0.8146 (t0) cc_final: 0.7638 (t70) REVERT: P 5 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7623 (ptt90) REVERT: P 53 ASP cc_start: 0.8689 (t0) cc_final: 0.8404 (t0) REVERT: P 76 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8515 (mmtm) REVERT: Q 80 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7571 (tptm) REVERT: S 33 TRP cc_start: 0.7505 (m100) cc_final: 0.6509 (m-10) REVERT: S 68 HIS cc_start: 0.4369 (OUTLIER) cc_final: 0.3758 (m-70) REVERT: T 52 GLU cc_start: 0.8243 (pp20) cc_final: 0.7629 (pp20) outliers start: 48 outliers final: 29 residues processed: 245 average time/residue: 0.2711 time to fit residues: 106.7160 Evaluate side-chains 229 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 36 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN C 68 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 51 GLN N 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.148061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112622 restraints weight = 92149.633| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.06 r_work: 0.3192 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 45985 Z= 0.211 Angle : 0.584 12.996 68910 Z= 0.296 Chirality : 0.033 0.267 8827 Planarity : 0.004 0.056 3644 Dihedral : 23.209 177.864 23289 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.74 % Favored : 89.02 % Rotamer: Outliers : 3.91 % Allowed : 22.21 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.16 (0.20), residues: 1630 helix: -0.04 (0.22), residues: 563 sheet: -1.78 (0.31), residues: 299 loop : -2.38 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 52 TYR 0.019 0.002 TYR D 3 PHE 0.014 0.001 PHE M 62 TRP 0.009 0.002 TRP C 200 HIS 0.005 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00413 (45985) covalent geometry : angle 0.58379 (68910) hydrogen bonds : bond 0.06137 ( 1361) hydrogen bonds : angle 3.17455 ( 2794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7026 (m-80) cc_final: 0.6621 (m-80) REVERT: C 48 LYS cc_start: 0.7420 (tptt) cc_final: 0.6903 (tppt) REVERT: C 165 GLU cc_start: 0.8197 (tp30) cc_final: 0.7834 (tp30) REVERT: D 130 ASN cc_start: 0.8926 (p0) cc_final: 0.8594 (p0) REVERT: E 71 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (tt) REVERT: E 85 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8270 (tttm) REVERT: I 114 LYS cc_start: 0.8817 (mppt) cc_final: 0.8486 (mptt) REVERT: I 118 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6477 (ttt90) REVERT: J 31 ARG cc_start: 0.5475 (tpp80) cc_final: 0.4821 (ptp-110) REVERT: J 88 MET cc_start: 0.6867 (mmm) cc_final: 0.6384 (mmm) REVERT: L 49 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6513 (mmp-170) REVERT: M 86 ARG cc_start: 0.2912 (tpt90) cc_final: 0.2458 (tpt170) REVERT: N 11 LYS cc_start: 0.7045 (ptmm) cc_final: 0.6510 (mtmt) REVERT: N 20 PHE cc_start: 0.3649 (OUTLIER) cc_final: 0.3169 (t80) REVERT: N 22 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5653 (pptt) REVERT: N 41 TRP cc_start: 0.6021 (p90) cc_final: 0.5236 (m-90) REVERT: N 91 GLU cc_start: 0.7955 (mt-10) cc_final: 0.6672 (mp0) REVERT: O 48 ASP cc_start: 0.8135 (t0) cc_final: 0.7731 (t70) REVERT: P 53 ASP cc_start: 0.8765 (t0) cc_final: 0.8479 (t0) REVERT: P 76 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8579 (mmtt) REVERT: Q 54 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8577 (mt) REVERT: Q 80 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7637 (tptm) REVERT: S 33 TRP cc_start: 0.7493 (m100) cc_final: 0.6558 (m-10) REVERT: S 68 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.3812 (m-70) REVERT: T 52 GLU cc_start: 0.8335 (pp20) cc_final: 0.7679 (pp20) outliers start: 51 outliers final: 36 residues processed: 228 average time/residue: 0.2859 time to fit residues: 103.0268 Evaluate side-chains 230 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 54 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 104 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN C 68 HIS C 189 HIS D 151 GLN E 60 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.144055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108671 restraints weight = 90916.772| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.47 r_work: 0.3126 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 45985 Z= 0.413 Angle : 0.816 12.063 68910 Z= 0.405 Chirality : 0.042 0.347 8827 Planarity : 0.006 0.084 3644 Dihedral : 23.476 179.110 23289 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.15 % Favored : 87.48 % Rotamer: Outliers : 4.98 % Allowed : 21.52 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.73 (0.20), residues: 1630 helix: -0.67 (0.21), residues: 576 sheet: -2.17 (0.29), residues: 305 loop : -2.55 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 52 TYR 0.024 0.003 TYR D 50 PHE 0.026 0.002 PHE P 32 TRP 0.014 0.002 TRP C 200 HIS 0.007 0.002 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00812 (45985) covalent geometry : angle 0.81629 (68910) hydrogen bonds : bond 0.08778 ( 1361) hydrogen bonds : angle 3.66487 ( 2794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 192 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7029 (m-80) cc_final: 0.6489 (m-80) REVERT: C 48 LYS cc_start: 0.7459 (tptt) cc_final: 0.6980 (tppt) REVERT: C 133 MET cc_start: 0.8140 (tmm) cc_final: 0.7844 (tmm) REVERT: C 165 GLU cc_start: 0.8255 (tp30) cc_final: 0.7801 (tp30) REVERT: E 71 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7994 (tt) REVERT: E 85 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8400 (tttm) REVERT: I 118 ARG cc_start: 0.7405 (mtm110) cc_final: 0.6739 (ttt90) REVERT: J 31 ARG cc_start: 0.5639 (tpp80) cc_final: 0.4850 (ptp-110) REVERT: J 66 GLU cc_start: 0.8523 (pp20) cc_final: 0.7962 (pp20) REVERT: J 88 MET cc_start: 0.6733 (mmm) cc_final: 0.6286 (mmm) REVERT: L 49 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6266 (mmp-170) REVERT: M 70 ARG cc_start: 0.5377 (mmp-170) cc_final: 0.4333 (mmt180) REVERT: N 2 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5572 (ttpt) REVERT: N 11 LYS cc_start: 0.7060 (ptmm) cc_final: 0.6558 (mtmt) REVERT: O 48 ASP cc_start: 0.8277 (t0) cc_final: 0.8048 (t70) REVERT: P 5 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7805 (ptt90) REVERT: P 53 ASP cc_start: 0.8757 (t0) cc_final: 0.8479 (t0) REVERT: P 76 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8628 (mtpt) REVERT: Q 80 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7779 (tptm) REVERT: S 68 HIS cc_start: 0.4605 (OUTLIER) cc_final: 0.3977 (m-70) REVERT: T 52 GLU cc_start: 0.8526 (pp20) cc_final: 0.7841 (pp20) REVERT: T 54 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 65 outliers final: 44 residues processed: 241 average time/residue: 0.2826 time to fit residues: 108.5888 Evaluate side-chains 233 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 132 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 278 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 227 optimal weight: 0.0270 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN C 68 HIS D 151 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** 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 = 0.4146 r_free = 0.4146 target = 0.147146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114564 restraints weight = 90865.924| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.62 r_work: 0.3215 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45985 Z= 0.209 Angle : 0.616 12.192 68910 Z= 0.315 Chirality : 0.035 0.267 8827 Planarity : 0.005 0.049 3644 Dihedral : 23.340 179.454 23289 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % Rotamer: Outliers : 3.75 % Allowed : 23.12 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.37 (0.20), residues: 1630 helix: -0.25 (0.22), residues: 565 sheet: -1.89 (0.32), residues: 275 loop : -2.47 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 52 TYR 0.020 0.002 TYR D 3 PHE 0.012 0.001 PHE M 62 TRP 0.010 0.001 TRP C 166 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00406 (45985) covalent geometry : angle 0.61596 (68910) hydrogen bonds : bond 0.06513 ( 1361) hydrogen bonds : angle 3.34164 ( 2794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7019 (m-80) cc_final: 0.6596 (m-80) REVERT: C 48 LYS cc_start: 0.7578 (tptt) cc_final: 0.7053 (tppt) REVERT: C 133 MET cc_start: 0.8090 (tmm) cc_final: 0.7816 (tmm) REVERT: C 165 GLU cc_start: 0.8131 (tp30) cc_final: 0.7768 (tp30) REVERT: E 71 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7950 (tt) REVERT: E 85 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8378 (tttm) REVERT: I 114 LYS cc_start: 0.8836 (mppt) cc_final: 0.8547 (mptt) REVERT: I 118 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6718 (ttt90) REVERT: J 88 MET cc_start: 0.6774 (mmm) cc_final: 0.6262 (mmm) REVERT: L 49 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6728 (mmp-170) REVERT: M 70 ARG cc_start: 0.5301 (mmp-170) cc_final: 0.4207 (mmt180) REVERT: M 86 ARG cc_start: 0.3282 (tpt90) cc_final: 0.2924 (tpt170) REVERT: N 5 MET cc_start: 0.4698 (ptp) cc_final: 0.3986 (ptp) REVERT: N 41 TRP cc_start: 0.6172 (p90) cc_final: 0.5405 (m-90) REVERT: N 91 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7682 (mt-10) REVERT: O 48 ASP cc_start: 0.8166 (t0) cc_final: 0.7867 (t70) REVERT: P 5 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7772 (ptt90) REVERT: P 53 ASP cc_start: 0.8770 (t0) cc_final: 0.8512 (t0) REVERT: P 76 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8617 (mmtm) REVERT: Q 54 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8576 (mt) REVERT: Q 80 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7635 (tptm) REVERT: S 68 HIS cc_start: 0.4644 (OUTLIER) cc_final: 0.4096 (m-70) REVERT: T 52 GLU cc_start: 0.8334 (pp20) cc_final: 0.7650 (pp20) REVERT: T 54 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8170 (tm-30) outliers start: 49 outliers final: 37 residues processed: 217 average time/residue: 0.2767 time to fit residues: 96.9549 Evaluate side-chains 219 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 25 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 243 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN C 68 HIS E 60 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** 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 = 0.4130 r_free = 0.4130 target = 0.145984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110224 restraints weight = 91352.107| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 45985 Z= 0.275 Angle : 0.663 11.898 68910 Z= 0.335 Chirality : 0.037 0.292 8827 Planarity : 0.005 0.050 3644 Dihedral : 23.359 179.156 23289 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.53 % Favored : 88.16 % Rotamer: Outliers : 4.06 % Allowed : 22.97 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.41 (0.20), residues: 1630 helix: -0.30 (0.22), residues: 565 sheet: -1.92 (0.32), residues: 275 loop : -2.49 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 52 TYR 0.020 0.002 TYR D 3 PHE 0.014 0.001 PHE P 32 TRP 0.009 0.002 TRP C 200 HIS 0.015 0.002 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00537 (45985) covalent geometry : angle 0.66290 (68910) hydrogen bonds : bond 0.07061 ( 1361) hydrogen bonds : angle 3.42469 ( 2794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10404.92 seconds wall clock time: 179 minutes 26.23 seconds (10766.23 seconds total)