Starting phenix.real_space_refine on Tue Sep 15 15:40:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w7n_21572/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_2026/6w7n_21572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w7n_21572/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 8.15, per 1000 atoms: 0.19 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: 3.31 Conformation dependent library (CDL) restraints added in 774.8 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: 5.99 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: 14.35 Time building geometry restraints manager: 4.64 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=" C3' A A1101 " pdb=" O3' A A1101 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C3' G A1300 " pdb=" O3' G A1300 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C3' A A1201 " pdb=" O3' A A1201 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.19e+00 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=" C3' G A 484 " pdb=" O3' G A 484 " ideal model delta sigma weight residual 1.415 1.444 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 45980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 64146 1.54 - 3.09: 3909 3.09 - 4.63: 622 4.63 - 6.18: 227 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 119.70 125.66 -5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C3' G A1300 " pdb=" O3' G A1300 " pdb=" P U A1301 " ideal model delta sigma weight residual 119.70 125.58 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" C3' A A 60 " pdb=" O3' A A 60 " pdb=" P G A 61 " ideal model delta sigma weight residual 119.70 125.51 -5.81 1.20e+00 6.94e-01 2.35e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 119.70 125.51 -5.81 1.20e+00 6.94e-01 2.34e+01 angle pdb=" C3' G A 484 " pdb=" O3' G A 484 " pdb=" P U A 485 " ideal model delta sigma weight residual 119.70 125.32 -5.62 1.20e+00 6.94e-01 2.19e+01 ... (remaining 68905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 22147 35.02 - 70.05: 2183 70.05 - 105.07: 191 105.07 - 140.09: 1 140.09 - 175.12: 6 Dihedral angle restraints: 24528 sinusoidal: 19781 harmonic: 4747 Sorted by residual: dihedral pdb=" C4' U A 960 " pdb=" C3' U A 960 " pdb=" C2' U A 960 " pdb=" C1' U A 960 " ideal model delta sinusoidal sigma weight residual 36.34 -38.43 74.77 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' A A 913 " pdb=" C3' A A 913 " pdb=" C2' A A 913 " pdb=" C1' A A 913 " ideal model delta sinusoidal sigma weight residual 36.34 -37.69 74.03 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' A A 499 " pdb=" C3' A A 499 " pdb=" C2' A A 499 " pdb=" C1' A A 499 " ideal model delta sinusoidal sigma weight residual 36.34 -37.46 73.81 1 3.10e+00 1.04e-01 7.20e+02 ... (remaining 24525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 6850 0.071 - 0.143: 260 0.143 - 0.214: 50 0.214 - 0.285: 1647 0.285 - 0.357: 20 Chirality restraints: 8827 Sorted by residual: chirality pdb=" P U A1202 " pdb=" OP1 U A1202 " pdb=" OP2 U A1202 " pdb=" O5' U A1202 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" P A A 329 " pdb=" OP1 A A 329 " pdb=" OP2 A A 329 " pdb=" O5' A A 329 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" P U A1301 " pdb=" OP1 U A1301 " pdb=" OP2 U A1301 " pdb=" O5' U A1301 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.71e+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: 2.010 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: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 44.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.003 0.036 45985 Z= 0.140 Angle : 0.850 7.720 68910 Z= 0.359 Chirality : 0.109 0.357 8827 Planarity : 0.003 0.035 3644 Dihedral : 20.053 175.117 21462 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/Z covalent geometry : bond 0.00272 / 0.14 (45985) covalent geometry : angle 0.84998 / 0.36 (68910) hydrogen bonds : bond 0.12753 / 6.53 ( 1361) hydrogen bonds : angle 4.83704 / 1.94 ( 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 : 0.864 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: 0.3372 time to fit residues: 163.5715 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 : 0.824 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 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: 4.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 HIS C 18 ASN C 40 GLN C 68 HIS C 175 HIS D 39 GLN D 119 HIS E 82 HIS E 147 ASN H 3 GLN I 4 GLN I 30 ASN I 31 GLN L 4 ASN L 45 ASN L 95 HIS 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.151190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112584 restraints weight = 93156.669| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.13 r_work: 0.3219 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 45985 Z= 0.346 Angle : 1.368 24.191 68910 Z= 0.541 Chirality : 0.107 1.294 8827 Planarity : 0.005 0.055 3644 Dihedral : 18.614 179.986 18311 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.49 % Favored : 89.26 % Rotamer: Outliers : 3.06 % Allowed : 13.86 % Favored : 83.08 % 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: -3.47 (0.19), residues: 1630 helix: -1.24 (0.21), residues: 575 sheet: -2.75 (0.28), residues: 294 loop : -2.95 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 114 TYR 0.019 0.002 TYR D 50 PHE 0.016 0.002 PHE S 73 TRP 0.017 0.002 TRP S 33 HIS 0.009 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.35 (45985) covalent geometry : angle 1.36818 / 0.54 (68910) hydrogen bonds : bond 0.08026 / 4.17 ( 1361) hydrogen bonds : angle 3.61114 / 1.47 ( 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: 40 poor density : 228 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7017 (m-80) cc_final: 0.6739 (m-80) REVERT: C 165 GLU cc_start: 0.8039 (tp30) cc_final: 0.7569 (tm-30) REVERT: D 173 ASP cc_start: 0.7574 (t0) cc_final: 0.7374 (t0) REVERT: E 85 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8381 (tttm) REVERT: H 117 GLN cc_start: 0.8839 (tt0) cc_final: 0.8346 (mt0) REVERT: I 118 ARG cc_start: 0.6637 (mtm110) cc_final: 0.5428 (ttt90) REVERT: J 31 ARG cc_start: 0.5660 (tpp80) cc_final: 0.4955 (ptp-110) REVERT: M 70 ARG cc_start: 0.5452 (mmp-170) cc_final: 0.4339 (mmt180) REVERT: M 78 ARG cc_start: 0.5060 (ptt90) cc_final: 0.4497 (pmt-80) REVERT: N 5 MET cc_start: 0.4788 (ptp) cc_final: 0.4396 (ptp) REVERT: N 11 LYS cc_start: 0.6896 (ptmm) cc_final: 0.6428 (mttt) REVERT: N 20 PHE cc_start: 0.3908 (OUTLIER) cc_final: 0.3603 (m-80) REVERT: N 88 MET cc_start: 0.8017 (mmt) cc_final: 0.7707 (mmm) REVERT: O 48 ASP cc_start: 0.8317 (t0) cc_final: 0.7871 (t70) REVERT: O 70 LYS cc_start: 0.8429 (tppp) cc_final: 0.7618 (tmmt) REVERT: P 53 ASP cc_start: 0.8865 (t0) cc_final: 0.8589 (t0) REVERT: P 76 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8412 (mmtt) REVERT: Q 80 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7466 (tptm) REVERT: T 52 GLU cc_start: 0.8280 (pp20) cc_final: 0.7760 (pp20) outliers start: 40 outliers final: 31 residues processed: 254 average time/residue: 0.3034 time to fit residues: 120.9612 Evaluate side-chains 236 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 GLU 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 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 20 PHE 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 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: 4.9990 chunk 183 optimal weight: 0.0270 chunk 252 optimal weight: 30.0000 chunk 230 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS E 60 GLN H 75 GLN L 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.154735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.117594 restraints weight = 94447.093| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.08 r_work: 0.3338 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 45985 Z= 0.175 Angle : 1.024 16.445 68910 Z= 0.412 Chirality : 0.084 1.062 8827 Planarity : 0.004 0.048 3644 Dihedral : 18.592 179.266 18311 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.98 % Favored : 91.84 % Rotamer: Outliers : 2.83 % Allowed : 17.61 % Favored : 79.56 % 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: -2.82 (0.20), residues: 1630 helix: -0.58 (0.22), residues: 568 sheet: -2.30 (0.29), residues: 288 loop : -2.71 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 91 TYR 0.014 0.001 TYR E 127 PHE 0.017 0.001 PHE D 181 TRP 0.008 0.001 TRP C 200 HIS 0.010 0.001 HIS M 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (45985) covalent geometry : angle 1.02423 / 0.41 (68910) hydrogen bonds : bond 0.06537 / 3.37 ( 1361) hydrogen bonds : angle 3.22292 / 1.32 ( 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 265 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7093 (m-80) cc_final: 0.6655 (m-80) REVERT: C 84 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6676 (tp30) REVERT: C 165 GLU cc_start: 0.8096 (tp30) cc_final: 0.7518 (tm-30) REVERT: D 130 ASN cc_start: 0.9001 (p0) cc_final: 0.8661 (p0) REVERT: E 71 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 85 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8282 (tttm) REVERT: H 117 GLN cc_start: 0.8756 (tt0) cc_final: 0.8368 (mt0) REVERT: I 118 ARG cc_start: 0.6627 (mtm110) cc_final: 0.5537 (ttt90) REVERT: J 31 ARG cc_start: 0.5374 (tpp80) cc_final: 0.4794 (ptp-110) REVERT: J 66 GLU cc_start: 0.8592 (pp20) cc_final: 0.8262 (pp20) REVERT: L 49 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6244 (mmp-170) REVERT: N 5 MET cc_start: 0.4446 (ptp) cc_final: 0.4123 (ptp) REVERT: N 11 LYS cc_start: 0.6973 (ptmm) cc_final: 0.6497 (mtmt) REVERT: N 59 GLN cc_start: 0.6566 (mp10) cc_final: 0.6294 (mp10) REVERT: N 88 MET cc_start: 0.8093 (mmt) cc_final: 0.7846 (mmm) REVERT: O 48 ASP cc_start: 0.8242 (t0) cc_final: 0.7811 (t70) REVERT: O 70 LYS cc_start: 0.8570 (tppp) cc_final: 0.7702 (tmtt) REVERT: P 53 ASP cc_start: 0.8789 (t0) cc_final: 0.8514 (t0) REVERT: P 76 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8429 (mmtm) REVERT: S 33 TRP cc_start: 0.7453 (m100) cc_final: 0.6753 (m100) REVERT: T 52 GLU cc_start: 0.8290 (pp20) cc_final: 0.7752 (pp20) outliers start: 37 outliers final: 21 residues processed: 246 average time/residue: 0.2909 time to fit residues: 113.6165 Evaluate side-chains 230 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 110 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 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 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: 6.9990 chunk 73 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 221 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.151885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114804 restraints weight = 93657.125| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.10 r_work: 0.3273 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 45985 Z= 0.233 Angle : 1.068 18.026 68910 Z= 0.429 Chirality : 0.085 1.213 8827 Planarity : 0.005 0.043 3644 Dihedral : 18.478 179.950 18311 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.18 % Favored : 89.63 % Rotamer: Outliers : 3.60 % Allowed : 18.38 % Favored : 78.02 % 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: -2.62 (0.20), residues: 1630 helix: -0.41 (0.22), residues: 568 sheet: -2.17 (0.30), residues: 290 loop : -2.60 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 5 TYR 0.013 0.002 TYR D 50 PHE 0.024 0.002 PHE I 102 TRP 0.009 0.001 TRP C 200 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (45985) covalent geometry : angle 1.06785 / 0.43 (68910) hydrogen bonds : bond 0.06890 / 3.55 ( 1361) hydrogen bonds : angle 3.25451 / 1.33 ( 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 263 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6902 (m-80) cc_final: 0.6465 (m-80) REVERT: C 54 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7516 (mp) REVERT: C 165 GLU cc_start: 0.8149 (tp30) cc_final: 0.7659 (tp30) REVERT: E 71 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8030 (tt) REVERT: E 85 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8296 (tttm) REVERT: I 74 GLN cc_start: 0.6843 (mt0) cc_final: 0.5886 (mm110) REVERT: I 118 ARG cc_start: 0.6741 (mtm110) cc_final: 0.5947 (ttt90) REVERT: J 31 ARG cc_start: 0.5648 (tpp80) cc_final: 0.5195 (ptp-110) REVERT: J 66 GLU cc_start: 0.8575 (pp20) cc_final: 0.8269 (pp20) REVERT: L 49 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6408 (mmp-170) REVERT: L 56 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (mp) REVERT: M 70 ARG cc_start: 0.5449 (mmp-170) cc_final: 0.4408 (mmt180) REVERT: M 86 ARG cc_start: 0.3239 (tpt90) cc_final: 0.2329 (tpt-90) REVERT: N 5 MET cc_start: 0.4574 (ptp) cc_final: 0.4219 (ptp) REVERT: N 11 LYS cc_start: 0.6992 (ptmm) cc_final: 0.6525 (mtmt) REVERT: O 44 GLU cc_start: 0.6895 (mp0) cc_final: 0.6215 (mp0) REVERT: O 48 ASP cc_start: 0.8244 (t0) cc_final: 0.7787 (t70) REVERT: P 53 ASP cc_start: 0.8800 (t0) cc_final: 0.8516 (t0) REVERT: P 76 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8484 (mmtm) REVERT: Q 80 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7301 (tptm) REVERT: S 33 TRP cc_start: 0.7424 (m100) cc_final: 0.6863 (m-10) REVERT: S 43 MET cc_start: 0.2339 (ttp) cc_final: 0.1725 (tmm) REVERT: T 52 GLU cc_start: 0.8388 (pp20) cc_final: 0.7790 (pp20) REVERT: T 54 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 47 outliers final: 36 residues processed: 243 average time/residue: 0.2806 time to fit residues: 108.1993 Evaluate side-chains 245 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE 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 C residue 191 THR 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 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 I residue 115 VAL Chi-restraints excluded: chain J residue 71 LEU 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 L residue 56 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 16 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 292 optimal weight: 6.9990 chunk 198 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 187 optimal weight: 0.0770 chunk 132 optimal weight: 20.0000 chunk 272 optimal weight: 1.9990 chunk 204 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS D 119 HIS E 60 GLN E 69 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS N 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.152559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117158 restraints weight = 93797.428| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.03 r_work: 0.3287 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45985 Z= 0.184 Angle : 0.995 16.008 68910 Z= 0.400 Chirality : 0.080 1.044 8827 Planarity : 0.004 0.040 3644 Dihedral : 18.444 178.023 18311 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.47 % Favored : 91.29 % Rotamer: Outliers : 4.13 % Allowed : 18.99 % 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: -2.31 (0.20), residues: 1630 helix: -0.11 (0.22), residues: 569 sheet: -2.02 (0.30), residues: 295 loop : -2.46 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG M 89 TYR 0.017 0.001 TYR D 3 PHE 0.014 0.001 PHE M 62 TRP 0.007 0.001 TRP C 200 HIS 0.005 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (45985) covalent geometry : angle 0.99479 / 0.40 (68910) hydrogen bonds : bond 0.06536 / 3.36 ( 1361) hydrogen bonds : angle 3.08648 / 1.26 ( 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 265 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6975 (m-80) cc_final: 0.6562 (m-80) REVERT: C 48 LYS cc_start: 0.7141 (tptt) cc_final: 0.6669 (tppt) REVERT: C 165 GLU cc_start: 0.7982 (tp30) cc_final: 0.7512 (tp30) REVERT: D 130 ASN cc_start: 0.8915 (p0) cc_final: 0.8624 (p0) REVERT: E 71 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8021 (tt) REVERT: E 85 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8232 (tttm) REVERT: I 118 ARG cc_start: 0.6836 (mtm110) cc_final: 0.6098 (ttt90) REVERT: J 31 ARG cc_start: 0.5577 (tpp80) cc_final: 0.5028 (ptp-110) REVERT: J 66 GLU cc_start: 0.8593 (pp20) cc_final: 0.8292 (pp20) REVERT: L 49 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6364 (mmp-170) REVERT: M 86 ARG cc_start: 0.2851 (tpt90) cc_final: 0.1989 (tpt-90) REVERT: M 90 HIS cc_start: 0.5386 (t70) cc_final: 0.4833 (t-90) REVERT: N 11 LYS cc_start: 0.7028 (ptmm) cc_final: 0.6566 (mtmt) REVERT: N 41 TRP cc_start: 0.5709 (p90) cc_final: 0.5022 (m-10) REVERT: N 59 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6425 (mp10) REVERT: N 88 MET cc_start: 0.8101 (mmp) cc_final: 0.7868 (mmm) REVERT: N 91 GLU cc_start: 0.7949 (mt-10) cc_final: 0.6484 (mp0) REVERT: O 44 GLU cc_start: 0.6697 (mp0) cc_final: 0.6176 (mp0) REVERT: O 48 ASP cc_start: 0.8154 (t0) cc_final: 0.7747 (t70) REVERT: P 53 ASP cc_start: 0.8700 (t0) cc_final: 0.8428 (t0) REVERT: P 76 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8530 (mmtm) REVERT: Q 80 LYS cc_start: 0.7834 (mmmm) cc_final: 0.7550 (tptm) REVERT: S 33 TRP cc_start: 0.7302 (m100) cc_final: 0.6469 (m-10) REVERT: S 43 MET cc_start: 0.2507 (ttp) cc_final: 0.1840 (tmm) REVERT: T 52 GLU cc_start: 0.8326 (pp20) cc_final: 0.7742 (pp20) REVERT: T 54 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8239 (tm-30) outliers start: 54 outliers final: 33 residues processed: 245 average time/residue: 0.2819 time to fit residues: 109.4133 Evaluate side-chains 235 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 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 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 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain M residue 74 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 196 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 7 ASN C 68 HIS C 189 HIS D 119 HIS D 151 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.148512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118976 restraints weight = 93482.043| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.28 r_work: 0.3224 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 45985 Z= 0.316 Angle : 1.156 21.337 68910 Z= 0.465 Chirality : 0.089 1.059 8827 Planarity : 0.005 0.065 3644 Dihedral : 18.544 178.499 18311 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.86 % Favored : 88.83 % Rotamer: Outliers : 4.44 % Allowed : 20.06 % Favored : 75.50 % 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: -2.50 (0.20), residues: 1630 helix: -0.35 (0.22), residues: 570 sheet: -2.05 (0.31), residues: 280 loop : -2.53 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 39 TYR 0.017 0.002 TYR D 3 PHE 0.019 0.002 PHE M 62 TRP 0.010 0.002 TRP C 200 HIS 0.006 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.32 (45985) covalent geometry : angle 1.15632 / 0.47 (68910) hydrogen bonds : bond 0.07737 / 4.01 ( 1361) hydrogen bonds : angle 3.38970 / 1.39 ( 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 269 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7068 (m-80) cc_final: 0.6641 (m-80) REVERT: C 48 LYS cc_start: 0.7284 (tptt) cc_final: 0.6787 (tppt) REVERT: C 165 GLU cc_start: 0.8022 (tp30) cc_final: 0.7523 (tp30) REVERT: E 71 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8057 (tt) REVERT: E 85 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8282 (tttm) REVERT: I 74 GLN cc_start: 0.6974 (mt0) cc_final: 0.6381 (mm110) REVERT: I 118 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6336 (ttt90) REVERT: J 31 ARG cc_start: 0.5569 (tpp80) cc_final: 0.4987 (ptp-110) REVERT: L 49 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6319 (mmp-170) REVERT: M 70 ARG cc_start: 0.5414 (mmp-170) cc_final: 0.4215 (mmt180) REVERT: N 11 LYS cc_start: 0.7108 (ptmm) cc_final: 0.6568 (mtmt) REVERT: N 20 PHE cc_start: 0.4116 (OUTLIER) cc_final: 0.3725 (t80) REVERT: N 88 MET cc_start: 0.8326 (mmp) cc_final: 0.7907 (mmm) REVERT: N 91 GLU cc_start: 0.8143 (mt-10) cc_final: 0.6961 (mp0) REVERT: O 48 ASP cc_start: 0.8259 (t0) cc_final: 0.7858 (t70) REVERT: P 53 ASP cc_start: 0.8775 (t0) cc_final: 0.8477 (t0) REVERT: P 76 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8565 (mmtm) REVERT: Q 80 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7564 (tptm) REVERT: S 33 TRP cc_start: 0.7427 (m100) cc_final: 0.6827 (m100) REVERT: S 43 MET cc_start: 0.2291 (ttp) cc_final: 0.1762 (tmm) REVERT: S 55 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: S 68 HIS cc_start: 0.4221 (OUTLIER) cc_final: 0.3653 (m170) REVERT: T 52 GLU cc_start: 0.8390 (pp20) cc_final: 0.7733 (pp20) REVERT: T 54 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8248 (tm-30) outliers start: 58 outliers final: 44 residues processed: 249 average time/residue: 0.2849 time to fit residues: 113.0830 Evaluate side-chains 244 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 C residue 191 THR 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 E residue 110 MET 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 114 LYS 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 L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain N residue 20 PHE 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 Q residue 40 THR Chi-restraints excluded: chain S residue 55 GLN 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 29 THR 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: 1.9990 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS C 189 HIS E 60 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 90 HIS N 59 GLN S 68 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.152653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116514 restraints weight = 93663.804| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.05 r_work: 0.3294 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45985 Z= 0.157 Angle : 0.989 15.039 68910 Z= 0.398 Chirality : 0.079 0.964 8827 Planarity : 0.004 0.034 3644 Dihedral : 18.493 177.808 18311 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.16 % Favored : 91.60 % Rotamer: Outliers : 3.75 % Allowed : 21.67 % Favored : 74.58 % 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: -2.11 (0.20), residues: 1630 helix: 0.03 (0.23), residues: 569 sheet: -1.74 (0.32), residues: 273 loop : -2.40 (0.20), residues: 788 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 0.022 0.001 PHE H 65 TRP 0.016 0.001 TRP C 166 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (45985) covalent geometry : angle 0.98859 / 0.40 (68910) hydrogen bonds : bond 0.06569 / 3.38 ( 1361) hydrogen bonds : angle 3.09864 / 1.27 ( 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 247 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6999 (m-80) cc_final: 0.6694 (m-80) REVERT: C 48 LYS cc_start: 0.7313 (tptt) cc_final: 0.6806 (tppt) REVERT: C 101 ASN cc_start: 0.7370 (m110) cc_final: 0.7164 (m-40) REVERT: C 165 GLU cc_start: 0.7847 (tp30) cc_final: 0.7444 (tm-30) REVERT: D 130 ASN cc_start: 0.8910 (p0) cc_final: 0.8619 (p0) REVERT: E 71 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8019 (tt) REVERT: E 85 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8264 (tttm) REVERT: H 95 MET cc_start: 0.7794 (mtp) cc_final: 0.7592 (mtt) REVERT: I 74 GLN cc_start: 0.6783 (mt0) cc_final: 0.6018 (mm110) REVERT: I 118 ARG cc_start: 0.6930 (mtm110) cc_final: 0.6284 (ttt90) REVERT: J 31 ARG cc_start: 0.5537 (tpp80) cc_final: 0.4965 (ptp-110) REVERT: L 49 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6380 (mmp-170) REVERT: M 86 ARG cc_start: 0.2715 (tpt90) cc_final: 0.2051 (tpt-90) REVERT: M 90 HIS cc_start: 0.5510 (t70) cc_final: 0.5063 (t-90) REVERT: N 11 LYS cc_start: 0.6985 (ptmm) cc_final: 0.6489 (mtmt) REVERT: N 20 PHE cc_start: 0.3635 (OUTLIER) cc_final: 0.3363 (t80) REVERT: N 41 TRP cc_start: 0.5804 (p90) cc_final: 0.5123 (m-90) REVERT: N 88 MET cc_start: 0.8270 (mmp) cc_final: 0.7948 (mmm) REVERT: O 48 ASP cc_start: 0.8098 (t0) cc_final: 0.7713 (t70) REVERT: P 53 ASP cc_start: 0.8679 (t0) cc_final: 0.8449 (t0) REVERT: P 76 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8568 (mmtm) REVERT: Q 54 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8554 (mt) REVERT: Q 80 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7491 (tptm) REVERT: S 33 TRP cc_start: 0.7325 (m100) cc_final: 0.6718 (m-10) REVERT: S 43 MET cc_start: 0.2458 (ttp) cc_final: 0.1760 (tmm) REVERT: S 68 HIS cc_start: 0.4756 (OUTLIER) cc_final: 0.4250 (m-70) REVERT: T 52 GLU cc_start: 0.8336 (pp20) cc_final: 0.7701 (pp20) REVERT: T 54 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8216 (tm-30) outliers start: 49 outliers final: 32 residues processed: 230 average time/residue: 0.2835 time to fit residues: 103.5704 Evaluate side-chains 229 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 177 MET 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 110 MET 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 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 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 20 PHE 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 Q residue 54 ILE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 36 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 137 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS D 151 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 13 HIS N 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113521 restraints weight = 93333.911| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.02 r_work: 0.3225 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 45985 Z= 0.259 Angle : 1.076 16.165 68910 Z= 0.433 Chirality : 0.083 1.019 8827 Planarity : 0.005 0.050 3644 Dihedral : 18.477 179.589 18311 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.80 % Favored : 88.96 % Rotamer: Outliers : 4.21 % Allowed : 21.29 % Favored : 74.50 % 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: -2.17 (0.20), residues: 1630 helix: -0.02 (0.22), residues: 565 sheet: -1.76 (0.32), residues: 275 loop : -2.42 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 51 TYR 0.017 0.002 TYR D 3 PHE 0.021 0.002 PHE H 65 TRP 0.010 0.002 TRP S 33 HIS 0.010 0.001 HIS S 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (45985) covalent geometry : angle 1.07618 / 0.43 (68910) hydrogen bonds : bond 0.07203 / 3.72 ( 1361) hydrogen bonds : angle 3.24194 / 1.32 ( 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 250 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7041 (m-80) cc_final: 0.6728 (m-80) REVERT: C 48 LYS cc_start: 0.7348 (tptt) cc_final: 0.6852 (tppt) REVERT: C 101 ASN cc_start: 0.7287 (m110) cc_final: 0.7079 (m-40) REVERT: C 165 GLU cc_start: 0.7939 (tp30) cc_final: 0.7490 (tm-30) REVERT: D 8 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8424 (mm) REVERT: E 71 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8069 (tt) REVERT: E 85 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8266 (tttm) REVERT: I 74 GLN cc_start: 0.6942 (mt0) cc_final: 0.6252 (mm110) REVERT: I 118 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6380 (ttt90) REVERT: J 31 ARG cc_start: 0.5303 (tpp80) cc_final: 0.4792 (ptp-110) REVERT: J 88 MET cc_start: 0.6724 (mmm) cc_final: 0.6303 (mmm) REVERT: L 49 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6462 (mmp-170) REVERT: M 70 ARG cc_start: 0.5690 (mmp-170) cc_final: 0.4488 (mmt180) REVERT: M 86 ARG cc_start: 0.2796 (tpt90) cc_final: 0.2163 (tpt-90) REVERT: N 11 LYS cc_start: 0.7017 (ptmm) cc_final: 0.6516 (mtmt) REVERT: N 20 PHE cc_start: 0.3882 (OUTLIER) cc_final: 0.3447 (t80) REVERT: N 22 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5836 (pptt) REVERT: N 41 TRP cc_start: 0.5854 (p90) cc_final: 0.5146 (m-90) REVERT: N 88 MET cc_start: 0.8312 (mmp) cc_final: 0.7939 (mmm) REVERT: N 91 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7765 (mt-10) REVERT: O 48 ASP cc_start: 0.8202 (t0) cc_final: 0.7766 (t70) REVERT: P 53 ASP cc_start: 0.8741 (t0) cc_final: 0.8479 (t0) REVERT: P 76 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8564 (mmtm) REVERT: Q 54 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8566 (mt) REVERT: Q 80 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7549 (tptm) REVERT: S 33 TRP cc_start: 0.7321 (m100) cc_final: 0.6720 (m100) REVERT: S 55 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: S 68 HIS cc_start: 0.4945 (OUTLIER) cc_final: 0.4408 (m90) REVERT: T 52 GLU cc_start: 0.8357 (pp20) cc_final: 0.7708 (pp20) REVERT: T 54 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8282 (tm-30) outliers start: 55 outliers final: 41 residues processed: 235 average time/residue: 0.2832 time to fit residues: 106.3682 Evaluate side-chains 240 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 8 LEU 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 E residue 110 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain H residue 11 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 114 LYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 51 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 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 45 HIS 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 55 GLN Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR 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: 5.9990 chunk 247 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 104 ASN 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 = 0.4145 r_free = 0.4145 target = 0.145878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111779 restraints weight = 92468.190| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.91 r_work: 0.3167 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 45985 Z= 0.436 Angle : 1.309 24.253 68910 Z= 0.526 Chirality : 0.098 1.136 8827 Planarity : 0.006 0.076 3644 Dihedral : 18.813 178.500 18311 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.72 % Favored : 87.91 % Rotamer: Outliers : 4.82 % Allowed : 20.98 % Favored : 74.20 % 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: -2.75 (0.20), residues: 1630 helix: -0.64 (0.21), residues: 578 sheet: -2.16 (0.30), residues: 284 loop : -2.63 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 58 TYR 0.023 0.002 TYR D 50 PHE 0.022 0.002 PHE P 32 TRP 0.012 0.002 TRP C 200 HIS 0.007 0.002 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00900 / 0.44 (45985) covalent geometry : angle 1.30949 / 0.53 (68910) hydrogen bonds : bond 0.08965 / 4.69 ( 1361) hydrogen bonds : angle 3.63937 / 1.48 ( 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 251 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.7067 (m-80) cc_final: 0.6627 (m-80) REVERT: C 48 LYS cc_start: 0.7457 (tptt) cc_final: 0.6968 (tppt) REVERT: C 101 ASN cc_start: 0.7587 (m110) cc_final: 0.7355 (m-40) REVERT: C 165 GLU cc_start: 0.8168 (tp30) cc_final: 0.7600 (tp30) REVERT: D 8 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8428 (mm) REVERT: E 12 GLU cc_start: 0.7882 (pt0) cc_final: 0.7651 (pt0) REVERT: E 71 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8022 (tt) REVERT: E 85 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8273 (tttm) REVERT: I 74 GLN cc_start: 0.7273 (mt0) cc_final: 0.6596 (mm110) REVERT: I 118 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6622 (ttt90) REVERT: J 31 ARG cc_start: 0.5690 (tpp80) cc_final: 0.4914 (ptp-110) REVERT: J 88 MET cc_start: 0.6999 (mmm) cc_final: 0.6532 (mmm) REVERT: L 49 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6395 (mmp-170) REVERT: M 70 ARG cc_start: 0.5385 (mmp-170) cc_final: 0.4187 (mmt180) REVERT: M 90 HIS cc_start: 0.5815 (t70) cc_final: 0.5532 (t70) REVERT: N 5 MET cc_start: 0.4480 (ptp) cc_final: 0.3727 (ptp) REVERT: N 11 LYS cc_start: 0.7172 (ptmm) cc_final: 0.6640 (mtpt) REVERT: N 20 PHE cc_start: 0.3549 (OUTLIER) cc_final: 0.2873 (t80) REVERT: N 88 MET cc_start: 0.8320 (mmp) cc_final: 0.8028 (mmm) REVERT: N 91 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7901 (mt-10) REVERT: P 53 ASP cc_start: 0.8758 (t0) cc_final: 0.8477 (t0) REVERT: P 76 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8639 (mmtm) REVERT: Q 80 LYS cc_start: 0.7905 (mmmm) cc_final: 0.7684 (tptm) REVERT: S 55 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5941 (pm20) REVERT: S 68 HIS cc_start: 0.4912 (OUTLIER) cc_final: 0.4244 (m170) REVERT: T 52 GLU cc_start: 0.8441 (pp20) cc_final: 0.7800 (pp20) REVERT: T 54 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8387 (tm-30) outliers start: 63 outliers final: 46 residues processed: 231 average time/residue: 0.2709 time to fit residues: 101.9316 Evaluate side-chains 235 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 25 THR 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 C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 8 LEU 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 E residue 110 MET Chi-restraints excluded: chain E residue 113 VAL 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 51 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 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain N residue 20 PHE 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 Q residue 54 ILE Chi-restraints excluded: chain S residue 55 GLN 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 29 THR 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: 20.0000 chunk 12 optimal weight: 0.6980 chunk 250 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 278 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 266 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118759 restraints weight = 92441.592| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.98 r_work: 0.3339 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45985 Z= 0.147 Angle : 1.008 15.661 68910 Z= 0.407 Chirality : 0.079 0.956 8827 Planarity : 0.004 0.035 3644 Dihedral : 18.609 178.206 18311 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.08 % Favored : 90.67 % Rotamer: Outliers : 3.14 % Allowed : 23.12 % Favored : 73.74 % 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: -2.07 (0.20), residues: 1630 helix: 0.13 (0.23), residues: 557 sheet: -1.67 (0.32), residues: 275 loop : -2.42 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 51 TYR 0.020 0.001 TYR D 3 PHE 0.019 0.001 PHE H 65 TRP 0.018 0.001 TRP C 166 HIS 0.007 0.001 HIS P 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (45985) covalent geometry : angle 1.00835 / 0.41 (68910) hydrogen bonds : bond 0.06657 / 3.43 ( 1361) hydrogen bonds : angle 3.16735 / 1.31 ( 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 239 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6993 (m-80) cc_final: 0.6687 (m-80) REVERT: C 48 LYS cc_start: 0.7487 (tptt) cc_final: 0.6969 (tppt) REVERT: C 104 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7152 (tp30) REVERT: C 133 MET cc_start: 0.7976 (tmm) cc_final: 0.7638 (tmm) REVERT: C 165 GLU cc_start: 0.7861 (tp30) cc_final: 0.7255 (tm-30) REVERT: D 130 ASN cc_start: 0.8995 (p0) cc_final: 0.8753 (p0) REVERT: E 71 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7910 (tt) REVERT: E 85 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8306 (tttm) REVERT: H 95 MET cc_start: 0.7978 (mtp) cc_final: 0.7732 (mtt) REVERT: I 118 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6381 (ttt90) REVERT: J 31 ARG cc_start: 0.5369 (tpp80) cc_final: 0.4724 (ptp-110) REVERT: J 88 MET cc_start: 0.6741 (mmm) cc_final: 0.6258 (mmm) REVERT: L 49 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6356 (mmp-170) REVERT: M 70 ARG cc_start: 0.5325 (mmp-170) cc_final: 0.4329 (mmt180) REVERT: M 86 ARG cc_start: 0.2669 (tpt90) cc_final: 0.1720 (tpt90) REVERT: N 5 MET cc_start: 0.4306 (ptp) cc_final: 0.3600 (ptp) REVERT: N 20 PHE cc_start: 0.3521 (OUTLIER) cc_final: 0.3082 (t80) REVERT: N 41 TRP cc_start: 0.6075 (p90) cc_final: 0.5293 (m-90) REVERT: N 59 GLN cc_start: 0.6891 (mp10) cc_final: 0.6565 (mp10) REVERT: N 88 MET cc_start: 0.8383 (mmp) cc_final: 0.8154 (mmm) REVERT: N 91 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7671 (mt-10) REVERT: P 5 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7716 (ptt90) REVERT: P 76 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8487 (mmtm) REVERT: Q 54 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8559 (mt) REVERT: Q 80 LYS cc_start: 0.7752 (mmmm) cc_final: 0.7468 (tptm) REVERT: S 33 TRP cc_start: 0.7411 (m100) cc_final: 0.6819 (m100) REVERT: S 68 HIS cc_start: 0.4866 (OUTLIER) cc_final: 0.4338 (m90) REVERT: T 52 GLU cc_start: 0.8334 (pp20) cc_final: 0.7709 (pp20) REVERT: T 54 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8159 (tm-30) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.2876 time to fit residues: 101.9528 Evaluate side-chains 226 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 69 THR 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 177 MET 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 110 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 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 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL 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 11 ILE 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: 8.9990 chunk 143 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 240 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.149391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117184 restraints weight = 92278.327| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.65 r_work: 0.3253 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 45985 Z= 0.281 Angle : 1.101 15.947 68910 Z= 0.444 Chirality : 0.085 1.032 8827 Planarity : 0.005 0.050 3644 Dihedral : 18.614 178.524 18311 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.98 % Favored : 88.77 % Rotamer: Outliers : 3.37 % Allowed : 22.66 % Favored : 73.97 % 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: -2.23 (0.20), residues: 1630 helix: -0.09 (0.22), residues: 563 sheet: -1.82 (0.31), residues: 285 loop : -2.42 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 52 TYR 0.021 0.002 TYR D 3 PHE 0.019 0.001 PHE H 65 TRP 0.009 0.002 TRP S 33 HIS 0.005 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.28 (45985) covalent geometry : angle 1.10134 / 0.44 (68910) hydrogen bonds : bond 0.07403 / 3.83 ( 1361) hydrogen bonds : angle 3.31604 / 1.36 ( 2794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10429.31 seconds wall clock time: 179 minutes 29.51 seconds (10769.51 seconds total)