Starting phenix.real_space_refine on Mon Sep 14 17:46:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yt9_10914/09_2026/6yt9_10914.cif" } resolution = 2.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1040 5.49 5 Mg 56 5.21 5 S 28 5.16 5 C 16706 2.51 5 N 6236 2.21 5 O 9213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33279 Number of models: 1 Model: "" Number of chains: 17 Chain: "2" Number of atoms: 19228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 19228 Classifications: {'RNAv2': 894} Modifications used: {'rna2p_pur': 73, 'rna2p_pyr': 39, 'rna3p_pur': 456, 'rna3p_pyr': 326} Link IDs: {'rna2p': 112, 'rna3p': 781} Chain breaks: 3 Chain: "4" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3129 Classifications: {'RNAv2': 146} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 73, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 131} Chain: "c" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1079 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ARG:plan': 15, 'ASP:plan': 14, 'GLN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 16, 'TYR:plan': 4, 'GLU:plan': 9} Unresolved non-hydrogen planarities: 372 Chain: "e" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1592 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 200} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "f" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "l" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 836 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "p" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "r" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "s" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 434 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "u" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "v" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 389 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "2" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.93, per 1000 atoms: 0.18 Number of scatterers: 33279 At special positions: 0 Unit cell: (167.205, 188.505, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 1040 15.00 Mg 56 11.99 O 9213 8.00 N 6236 7.00 C 16706 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: 2.60 Conformation dependent library (CDL) restraints added in 717.8 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 41.3% alpha, 19.1% beta 368 base pairs and 597 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'c' and resid 11 through 15 removed outlier: 3.823A pdb=" N GLY c 15 " --> pdb=" O LEU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 30 removed outlier: 3.644A pdb=" N ARG c 30 " --> pdb=" O PRO c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 removed outlier: 3.981A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 88 removed outlier: 3.894A pdb=" N ARG c 83 " --> pdb=" O SER c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 120 removed outlier: 3.699A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG c 115 " --> pdb=" O GLN c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 removed outlier: 3.710A pdb=" N GLN c 124 " --> pdb=" O GLN c 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP c 125 " --> pdb=" O THR c 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 120 through 125' Processing helix chain 'c' and resid 135 through 151 removed outlier: 4.303A pdb=" N ARG c 139 " --> pdb=" O GLU c 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 181 Processing helix chain 'c' and resid 208 through 224 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.532A pdb=" N SER e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 66 Processing helix chain 'e' and resid 70 through 82 Processing helix chain 'e' and resid 87 through 98 Processing helix chain 'e' and resid 99 through 108 Processing helix chain 'e' and resid 114 through 122 removed outlier: 3.576A pdb=" N VAL e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 152 removed outlier: 3.774A pdb=" N LYS e 152 " --> pdb=" O GLU e 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 149 through 152' Processing helix chain 'e' and resid 154 through 165 removed outlier: 3.801A pdb=" N LYS e 158 " --> pdb=" O GLN e 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU e 163 " --> pdb=" O ASN e 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA e 165 " --> pdb=" O ILE e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 198 through 206 removed outlier: 4.064A pdb=" N ILE e 202 " --> pdb=" O ASN e 198 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 67 Processing helix chain 'f' and resid 108 through 117 removed outlier: 3.545A pdb=" N ALA f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 146 Processing helix chain 'f' and resid 148 through 157 Processing helix chain 'g' and resid 13 through 17 removed outlier: 4.080A pdb=" N ASP g 16 " --> pdb=" O ASP g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 31 removed outlier: 3.563A pdb=" N GLU g 23 " --> pdb=" O VAL g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 80 Processing helix chain 'i' and resid 6 through 20 Processing helix chain 'i' and resid 30 through 43 removed outlier: 3.617A pdb=" N VAL i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 120 Processing helix chain 'l' and resid 58 through 74 Processing helix chain 'l' and resid 75 through 77 No H-bonds generated for 'chain 'l' and resid 75 through 77' Processing helix chain 'l' and resid 92 through 100 removed outlier: 4.122A pdb=" N VAL l 96 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 Processing helix chain 'm' and resid 21 through 25 removed outlier: 3.543A pdb=" N LYS m 25 " --> pdb=" O PRO m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 118 removed outlier: 3.640A pdb=" N GLY m 118 " --> pdb=" O SER m 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 39 Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.681A pdb=" N ALA p 45 " --> pdb=" O GLY p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.553A pdb=" N ARG p 54 " --> pdb=" O HIS p 50 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 removed outlier: 3.590A pdb=" N TYR p 78 " --> pdb=" O ASP p 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 63 Processing helix chain 'q' and resid 68 through 78 Processing helix chain 's' and resid 25 through 30 Processing helix chain 's' and resid 31 through 33 No H-bonds generated for 'chain 's' and resid 31 through 33' Processing helix chain 's' and resid 41 through 46 Processing helix chain 's' and resid 48 through 65 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 Proline residue: u 56 - end of helix Processing helix chain 'u' and resid 68 through 85 removed outlier: 3.541A pdb=" N ALA u 85 " --> pdb=" O ALA u 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 26 removed outlier: 3.527A pdb=" N ARG v 17 " --> pdb=" O ASP v 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU v 24 " --> pdb=" O LYS v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 34 Processing helix chain 'v' and resid 40 through 60 Processing sheet with id=AA1, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.349A pdb=" N PHE c 18 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE c 43 " --> pdb=" O PHE c 18 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS c 20 " --> pdb=" O HIS c 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY c 35 " --> pdb=" O ILE c 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 93 through 94 removed outlier: 8.034A pdb=" N VAL c 94 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE c 71 " --> pdb=" O VAL c 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'f' and resid 11 through 23 removed outlier: 6.566A pdb=" N LEU f 35 " --> pdb=" O VAL f 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL f 17 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR f 33 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG f 19 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER f 31 " --> pdb=" O ARG f 19 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA f 21 " --> pdb=" O ILE f 29 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE f 29 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 84 through 88 removed outlier: 6.383A pdb=" N ILE f 105 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS f 126 " --> pdb=" O ILE f 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 35 through 46 removed outlier: 6.435A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU g 39 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU g 61 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP g 41 " --> pdb=" O TYR g 59 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR g 59 " --> pdb=" O ASP g 41 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY g 43 " --> pdb=" O ALA g 57 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA g 57 " --> pdb=" O GLY g 43 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS g 3 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG g 91 " --> pdb=" O HIS g 3 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU g 5 " --> pdb=" O ILE g 89 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE g 89 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL g 7 " --> pdb=" O ASN g 87 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN g 87 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU g 9 " --> pdb=" O ILE g 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 24 through 28 removed outlier: 6.168A pdb=" N THR i 59 " --> pdb=" O VAL i 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL i 51 " --> pdb=" O THR i 59 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR i 61 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL i 49 " --> pdb=" O THR i 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR i 63 " --> pdb=" O SER i 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 66 through 67 removed outlier: 3.739A pdb=" N LYS i 70 " --> pdb=" O PHE i 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 75 through 78 removed outlier: 5.583A pdb=" N VAL i 126 " --> pdb=" O SER i 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER i 106 " --> pdb=" O VAL i 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA i 128 " --> pdb=" O ILE i 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.821A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU l 81 " --> pdb=" O ILE l 106 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER l 108 " --> pdb=" O LEU l 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.649A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR m 97 " --> pdb=" O SER m 64 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR m 66 " --> pdb=" O THR m 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER m 78 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 50 through 51 removed outlier: 4.892A pdb=" N ILE q 19 " --> pdb=" O ILE q 36 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE q 38 " --> pdb=" O TYR q 17 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR q 17 " --> pdb=" O PHE q 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL q 2 " --> pdb=" O GLN q 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'r' and resid 8 through 15 removed outlier: 16.782A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 12.917A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) removed outlier: 15.857A pdb=" N LYS r 72 " --> pdb=" O SER r 42 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N LYS r 44 " --> pdb=" O LYS r 72 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N TRP r 74 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS r 46 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU r 76 " --> pdb=" O HIS r 46 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS r 48 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU r 78 " --> pdb=" O HIS r 48 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS r 72 " --> pdb=" O ILE r 68 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP r 74 " --> pdb=" O ARG r 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG r 66 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N LEU r 76 " --> pdb=" O GLU r 64 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU r 64 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU r 78 " --> pdb=" O ILE r 62 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE r 62 " --> pdb=" O GLU r 78 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL r 80 " --> pdb=" O VAL r 60 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL r 60 " --> pdb=" O VAL r 80 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 912 hydrogen bonds 1386 hydrogen bond angles 0 basepair planarities 368 basepair parallelities 597 stacking parallelities Total time for adding SS restraints: 13.67 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4078 1.32 - 1.44: 15122 1.44 - 1.56: 14711 1.56 - 1.69: 2075 1.69 - 1.81: 48 Bond restraints: 36034 Sorted by residual: bond pdb=" C ASP e 192 " pdb=" N LEU e 193 " ideal model delta sigma weight residual 1.333 1.280 0.052 2.74e-02 1.33e+03 3.63e+00 bond pdb=" CA GLY f 107 " pdb=" C GLY f 107 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.55e+00 bond pdb=" O3' A 41497 " pdb=" P C 41498 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" O3' A 2 570 " pdb=" P A 2 571 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.20e-02 6.94e+03 2.91e+00 bond pdb=" N3 C 2 172 " pdb=" C4 C 2 172 " ideal model delta sigma weight residual 1.334 1.301 0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 36029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 50712 2.21 - 4.43: 2774 4.43 - 6.64: 392 6.64 - 8.85: 13 8.85 - 11.06: 1 Bond angle restraints: 53892 Sorted by residual: angle pdb=" C3' G 2 186 " pdb=" O3' G 2 186 " pdb=" P G 2 187 " ideal model delta sigma weight residual 119.70 125.43 -5.73 1.20e+00 6.94e-01 2.28e+01 angle pdb=" C GLU f 54 " pdb=" N VAL f 55 " pdb=" CA VAL f 55 " ideal model delta sigma weight residual 120.33 123.93 -3.60 8.00e-01 1.56e+00 2.03e+01 angle pdb=" C2' G 2 100 " pdb=" C1' G 2 100 " pdb=" N9 G 2 100 " ideal model delta sigma weight residual 112.40 103.64 8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" C ALA f 106 " pdb=" N GLY f 107 " pdb=" CA GLY f 107 " ideal model delta sigma weight residual 122.73 118.85 3.88 9.30e-01 1.16e+00 1.74e+01 angle pdb=" O3' A 2 886 " pdb=" C3' A 2 886 " pdb=" C2' A 2 886 " ideal model delta sigma weight residual 113.80 106.06 7.74 2.00e+00 2.50e-01 1.50e+01 ... (remaining 53887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 17142 35.64 - 71.28: 1962 71.28 - 106.92: 117 106.92 - 142.55: 0 142.55 - 178.19: 1 Dihedral angle restraints: 19222 sinusoidal: 14936 harmonic: 4286 Sorted by residual: dihedral pdb=" C4' A 2 125 " pdb=" C3' A 2 125 " pdb=" C2' A 2 125 " pdb=" C1' A 2 125 " ideal model delta sinusoidal sigma weight residual 36.34 -42.32 78.66 1 3.10e+00 1.04e-01 8.03e+02 dihedral pdb=" C4' G 2 815 " pdb=" C3' G 2 815 " pdb=" C2' G 2 815 " pdb=" C1' G 2 815 " ideal model delta sinusoidal sigma weight residual 36.34 -41.08 77.43 1 3.10e+00 1.04e-01 7.81e+02 dihedral pdb=" C4' G 2 424 " pdb=" C3' G 2 424 " pdb=" C2' G 2 424 " pdb=" C1' G 2 424 " ideal model delta sinusoidal sigma weight residual 36.34 -40.45 76.79 1 3.10e+00 1.04e-01 7.71e+02 ... (remaining 19219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5223 0.088 - 0.175: 635 0.175 - 0.263: 878 0.263 - 0.350: 180 0.350 - 0.438: 3 Chirality restraints: 6919 Sorted by residual: chirality pdb=" C2' G 2 100 " pdb=" C3' G 2 100 " pdb=" O2' G 2 100 " pdb=" C1' G 2 100 " both_signs ideal model delta sigma weight residual False -2.79 -2.35 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C2' C 2 99 " pdb=" C3' C 2 99 " pdb=" O2' C 2 99 " pdb=" C1' C 2 99 " both_signs ideal model delta sigma weight residual False -2.79 -2.38 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C2' A 2 222 " pdb=" C3' A 2 222 " pdb=" O2' A 2 222 " pdb=" C1' A 2 222 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 6916 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 99 " 0.090 2.00e-02 2.50e+03 4.64e-02 4.84e+01 pdb=" N1 C 2 99 " -0.099 2.00e-02 2.50e+03 pdb=" C2 C 2 99 " -0.018 2.00e-02 2.50e+03 pdb=" O2 C 2 99 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 2 99 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 99 " 0.027 2.00e-02 2.50e+03 pdb=" C5 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C 2 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 100 " 0.087 2.00e-02 2.50e+03 3.87e-02 4.49e+01 pdb=" N9 G 2 100 " -0.097 2.00e-02 2.50e+03 pdb=" C8 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 2 100 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 100 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 100 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G 2 100 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.082 2.00e-02 2.50e+03 3.48e-02 3.62e+01 pdb=" N9 G 2 612 " -0.080 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.017 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 147 2.44 - 3.05: 19077 3.05 - 3.67: 62268 3.67 - 4.28: 98634 4.28 - 4.90: 129249 Nonbonded interactions: 309375 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.825 2.170 nonbonded pdb=" OP1 C 2 573 " pdb="MG MG 21651 " model vdw 1.936 2.170 nonbonded pdb=" OP1 A 41497 " pdb="MG MG 41602 " model vdw 1.944 2.170 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 1.948 2.170 nonbonded pdb=" OP2 U 2 557 " pdb="MG MG 21613 " model vdw 1.979 2.170 ... (remaining 309370 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.150 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.010 0.079 36034 Z= 0.494 Angle : 1.084 11.063 53892 Z= 0.461 Chirality : 0.105 0.438 6919 Planarity : 0.006 0.046 2984 Dihedral : 21.484 178.192 16456 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 8.22 % Allowed : 19.84 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.30 (0.18), residues: 1470 helix: -1.73 (0.18), residues: 594 sheet: -1.59 (0.29), residues: 249 loop : -2.83 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 24 TYR 0.021 0.003 TYR m 117 PHE 0.020 0.002 PHE e 184 TRP 0.013 0.003 TRP r 74 HIS 0.006 0.002 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.49 (36034) covalent geometry : angle 1.08417 / 0.46 (53892) hydrogen bonds : bond 0.11707 / 6.04 ( 1427) hydrogen bonds : angle 4.49766 / 1.81 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 251 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7507 (p-80) REVERT: e 167 ARG cc_start: 0.5447 (tmm160) cc_final: 0.4970 (ttp-170) REVERT: f 68 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6780 (mtm-85) REVERT: g 44 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7619 (ttm-80) REVERT: g 68 GLN cc_start: 0.7820 (tp40) cc_final: 0.7419 (tp-100) REVERT: i 41 GLN cc_start: 0.8263 (tt0) cc_final: 0.8003 (tt0) REVERT: m 88 LYS cc_start: 0.8588 (tptp) cc_final: 0.8335 (ttmm) REVERT: r 20 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7857 (pttt) outliers start: 82 outliers final: 51 residues processed: 313 average time/residue: 0.7828 time to fit residues: 287.4464 Evaluate side-chains 297 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 136 SER Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 68 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain g residue 102 LEU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 55 VAL Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 66 SER Chi-restraints excluded: chain u residue 27 MET Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 128 ASN e 148 HIS e 177 HIS g 17 GLN g 52 ASN g 63 ASN i 18 GLN i 41 GLN i 42 GLN i 98 GLN l 21 HIS l 37 GLN l 49 GLN l 107 ASN p 46 HIS p 62 GLN q 44 GLN u 6 GLN u 80 ASN v 57 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116151 restraints weight = 39570.425| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 0.33 r_work: 0.3117 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work: 0.2899 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36034 Z= 0.241 Angle : 1.356 25.709 53892 Z= 0.543 Chirality : 0.120 1.978 6919 Planarity : 0.005 0.038 2984 Dihedral : 18.791 171.351 14173 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.11 % Allowed : 25.35 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.84 (0.20), residues: 1470 helix: -0.16 (0.20), residues: 614 sheet: -1.29 (0.30), residues: 254 loop : -2.28 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 24 TYR 0.014 0.001 TYR m 117 PHE 0.013 0.001 PHE e 184 TRP 0.010 0.002 TRP q 60 HIS 0.005 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.24 (36034) covalent geometry : angle 1.35628 / 0.54 (53892) hydrogen bonds : bond 0.06775 / 3.49 ( 1427) hydrogen bonds : angle 3.28408 / 1.31 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7325 (p-80) REVERT: e 130 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6950 (ttm170) REVERT: e 167 ARG cc_start: 0.5791 (tmm160) cc_final: 0.5209 (ttp-170) REVERT: g 14 GLN cc_start: 0.7782 (mp-120) cc_final: 0.7439 (mm110) REVERT: g 63 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8637 (m110) REVERT: g 68 GLN cc_start: 0.7959 (tp40) cc_final: 0.7665 (tp-100) REVERT: g 96 ILE cc_start: 0.8463 (mm) cc_final: 0.7767 (mp) REVERT: i 19 MET cc_start: 0.8572 (mtm) cc_final: 0.8357 (mtm) REVERT: l 104 TYR cc_start: 0.7472 (m-80) cc_final: 0.7149 (m-80) REVERT: m 86 ARG cc_start: 0.8784 (ptt180) cc_final: 0.8458 (ppt-90) REVERT: p 22 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (m) REVERT: q 48 GLU cc_start: 0.7958 (tt0) cc_final: 0.7736 (tt0) REVERT: r 20 LYS cc_start: 0.8642 (ptpt) cc_final: 0.8241 (pttt) REVERT: s 35 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7563 (pt0) outliers start: 51 outliers final: 27 residues processed: 302 average time/residue: 0.7722 time to fit residues: 275.0471 Evaluate side-chains 279 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 63 ASN Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 138 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 91 ASN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 42 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN u 80 ASN v 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105692 restraints weight = 39621.257| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 0.36 r_work: 0.2971 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 36034 Z= 0.415 Angle : 1.349 20.731 53892 Z= 0.545 Chirality : 0.118 1.934 6919 Planarity : 0.005 0.042 2984 Dihedral : 19.040 179.854 14125 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 7.92 % Allowed : 24.35 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.40 (0.21), residues: 1470 helix: 0.31 (0.21), residues: 609 sheet: -1.05 (0.31), residues: 259 loop : -2.16 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG m 9 TYR 0.019 0.002 TYR m 117 PHE 0.019 0.002 PHE e 184 TRP 0.010 0.002 TRP r 74 HIS 0.004 0.001 HIS f 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.42 (36034) covalent geometry : angle 1.34874 / 0.55 (53892) hydrogen bonds : bond 0.07329 / 3.79 ( 1427) hydrogen bonds : angle 3.24772 / 1.31 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 249 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7462 (p-80) REVERT: e 56 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8630 (mt0) REVERT: e 130 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6874 (ttm170) REVERT: e 167 ARG cc_start: 0.5649 (tmm160) cc_final: 0.5290 (ttp-170) REVERT: e 208 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6310 (mtpp) REVERT: f 53 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7764 (tpp80) REVERT: g 31 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: g 68 GLN cc_start: 0.7899 (tp40) cc_final: 0.7653 (tp-100) REVERT: g 71 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7992 (tm) REVERT: g 96 ILE cc_start: 0.8151 (mm) cc_final: 0.7892 (mt) REVERT: m 43 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7953 (mtpp) REVERT: m 86 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8189 (ppt-90) REVERT: m 88 LYS cc_start: 0.8730 (tptp) cc_final: 0.8421 (ttmm) REVERT: p 22 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8159 (m) REVERT: q 48 GLU cc_start: 0.7734 (tt0) cc_final: 0.7494 (tt0) REVERT: r 20 LYS cc_start: 0.8630 (ptpt) cc_final: 0.8226 (pttt) REVERT: r 30 VAL cc_start: 0.8038 (m) cc_final: 0.7832 (m) REVERT: s 35 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7657 (pt0) outliers start: 79 outliers final: 43 residues processed: 306 average time/residue: 0.7888 time to fit residues: 283.0619 Evaluate side-chains 299 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 56 GLN Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 91 ASN e 177 HIS g 28 GLN g 52 ASN g 63 ASN i 41 GLN i 42 GLN l 107 ASN m 111 ASN p 37 ASN p 62 GLN u 3 ASN v 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110749 restraints weight = 39434.732| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.35 r_work: 0.3052 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36034 Z= 0.243 Angle : 1.142 19.555 53892 Z= 0.462 Chirality : 0.097 1.205 6919 Planarity : 0.004 0.039 2984 Dihedral : 19.133 179.431 14125 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.31 % Allowed : 26.15 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.86 (0.21), residues: 1470 helix: 0.83 (0.21), residues: 605 sheet: -0.80 (0.32), residues: 261 loop : -1.91 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 41 TYR 0.015 0.002 TYR m 117 PHE 0.015 0.002 PHE v 37 TRP 0.009 0.002 TRP q 60 HIS 0.003 0.001 HIS f 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 (36034) covalent geometry : angle 1.14200 / 0.46 (53892) hydrogen bonds : bond 0.06574 / 3.38 ( 1427) hydrogen bonds : angle 3.03517 / 1.22 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: e 130 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6853 (ttm170) REVERT: e 167 ARG cc_start: 0.5474 (tmm160) cc_final: 0.5130 (ttp-170) REVERT: f 40 ASP cc_start: 0.8426 (p0) cc_final: 0.8210 (p0) REVERT: f 53 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7798 (tpp80) REVERT: g 14 GLN cc_start: 0.7740 (mp-120) cc_final: 0.7491 (mm110) REVERT: g 71 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8040 (tm) REVERT: g 96 ILE cc_start: 0.8408 (mm) cc_final: 0.7883 (mp) REVERT: l 104 TYR cc_start: 0.7605 (m-80) cc_final: 0.7206 (m-80) REVERT: m 43 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7933 (mtpp) REVERT: m 86 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8348 (ppt-90) REVERT: q 48 GLU cc_start: 0.7695 (tt0) cc_final: 0.7414 (tt0) REVERT: r 20 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8275 (pttt) outliers start: 63 outliers final: 29 residues processed: 308 average time/residue: 0.8062 time to fit residues: 291.6450 Evaluate side-chains 286 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 168 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN v 57 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114323 restraints weight = 39659.355| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.31 r_work: 0.3099 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36034 Z= 0.182 Angle : 1.101 19.309 53892 Z= 0.446 Chirality : 0.094 1.125 6919 Planarity : 0.004 0.041 2984 Dihedral : 19.169 178.839 14112 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.51 % Allowed : 27.86 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.54 (0.22), residues: 1470 helix: 1.13 (0.22), residues: 605 sheet: -0.69 (0.33), residues: 261 loop : -1.76 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 38 TYR 0.012 0.001 TYR m 117 PHE 0.017 0.001 PHE v 37 TRP 0.009 0.001 TRP q 60 HIS 0.003 0.001 HIS g 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (36034) covalent geometry : angle 1.10089 / 0.45 (53892) hydrogen bonds : bond 0.06380 / 3.28 ( 1427) hydrogen bonds : angle 2.98247 / 1.19 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 260 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: e 130 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6858 (ttm170) REVERT: f 40 ASP cc_start: 0.8415 (p0) cc_final: 0.8172 (p0) REVERT: g 71 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7957 (tm) REVERT: g 96 ILE cc_start: 0.8414 (mm) cc_final: 0.7890 (mp) REVERT: i 70 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7677 (ptpp) REVERT: l 104 TYR cc_start: 0.7632 (m-80) cc_final: 0.7221 (m-80) REVERT: m 86 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8325 (ppt-90) REVERT: q 48 GLU cc_start: 0.7651 (tt0) cc_final: 0.7379 (tt0) REVERT: r 20 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8313 (pttt) REVERT: s 35 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7539 (pt0) outliers start: 55 outliers final: 35 residues processed: 295 average time/residue: 0.7647 time to fit residues: 265.8302 Evaluate side-chains 291 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 108 LYS Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 175 optimal weight: 0.0970 chunk 201 optimal weight: 0.8980 chunk 144 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN g 63 ASN i 41 GLN l 107 ASN m 111 ASN ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN p 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117328 restraints weight = 39798.792| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 0.33 r_work: 0.3145 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 36034 Z= 0.172 Angle : 1.032 18.909 53892 Z= 0.418 Chirality : 0.086 1.013 6919 Planarity : 0.004 0.043 2984 Dihedral : 19.113 179.468 14111 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.41 % Allowed : 28.56 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.11 (0.22), residues: 1470 helix: 1.45 (0.22), residues: 605 sheet: -0.37 (0.34), residues: 251 loop : -1.52 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 44 TYR 0.011 0.001 TYR m 117 PHE 0.018 0.001 PHE v 37 TRP 0.009 0.001 TRP q 60 HIS 0.004 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (36034) covalent geometry : angle 1.03201 / 0.42 (53892) hydrogen bonds : bond 0.06271 / 3.20 ( 1427) hydrogen bonds : angle 2.85197 / 1.14 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: e 130 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6902 (ttm170) REVERT: e 174 GLU cc_start: 0.7419 (pm20) cc_final: 0.6920 (pm20) REVERT: e 208 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5768 (mtpp) REVERT: f 47 PHE cc_start: 0.9031 (p90) cc_final: 0.8792 (p90) REVERT: f 53 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7718 (tpp80) REVERT: f 74 ASP cc_start: 0.6945 (t70) cc_final: 0.6542 (t0) REVERT: g 45 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8679 (mtp-110) REVERT: g 96 ILE cc_start: 0.8388 (mm) cc_final: 0.8183 (mt) REVERT: i 70 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7573 (ptpp) REVERT: l 104 TYR cc_start: 0.7582 (m-80) cc_final: 0.7162 (m-80) REVERT: l 106 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8206 (pp) REVERT: m 86 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (ppt-90) REVERT: q 48 GLU cc_start: 0.7653 (tt0) cc_final: 0.7376 (tt0) REVERT: r 20 LYS cc_start: 0.8658 (ptpt) cc_final: 0.8353 (ptmt) REVERT: r 40 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6910 (mtp85) REVERT: s 35 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7461 (pt0) outliers start: 54 outliers final: 21 residues processed: 290 average time/residue: 0.7584 time to fit residues: 258.7722 Evaluate side-chains 274 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 48 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110836 restraints weight = 39586.009| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.35 r_work: 0.3052 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work: 0.2817 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36034 Z= 0.271 Angle : 1.131 19.773 53892 Z= 0.458 Chirality : 0.095 1.128 6919 Planarity : 0.004 0.035 2984 Dihedral : 19.079 179.991 14106 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.91 % Allowed : 29.16 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.14 (0.22), residues: 1470 helix: 1.38 (0.21), residues: 605 sheet: -0.27 (0.34), residues: 249 loop : -1.53 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG s 43 TYR 0.014 0.002 TYR m 117 PHE 0.020 0.002 PHE v 37 TRP 0.008 0.002 TRP l 43 HIS 0.007 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (36034) covalent geometry : angle 1.13101 / 0.46 (53892) hydrogen bonds : bond 0.06551 / 3.36 ( 1427) hydrogen bonds : angle 2.92631 / 1.18 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: e 208 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.6024 (mtpp) REVERT: f 53 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7813 (tpp80) REVERT: g 31 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: g 96 ILE cc_start: 0.8456 (mm) cc_final: 0.7907 (mp) REVERT: l 104 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: m 43 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: m 86 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8430 (ppt-90) REVERT: q 48 GLU cc_start: 0.7876 (tt0) cc_final: 0.7594 (tt0) REVERT: r 20 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8363 (ptmt) REVERT: r 66 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8521 (ppt-90) REVERT: s 35 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: v 46 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7439 (mtmt) outliers start: 59 outliers final: 36 residues processed: 280 average time/residue: 0.7942 time to fit residues: 261.1344 Evaluate side-chains 287 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 66 ARG Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain v residue 46 LYS Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 168 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111628 restraints weight = 39426.251| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.31 r_work: 0.3040 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 36034 Z= 0.281 Angle : 1.144 19.787 53892 Z= 0.463 Chirality : 0.096 1.149 6919 Planarity : 0.004 0.035 2984 Dihedral : 19.127 179.973 14106 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.91 % Allowed : 28.96 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.19 (0.22), residues: 1470 helix: 1.35 (0.21), residues: 604 sheet: -0.40 (0.33), residues: 256 loop : -1.54 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 13 TYR 0.015 0.002 TYR m 117 PHE 0.021 0.002 PHE v 37 TRP 0.009 0.002 TRP l 43 HIS 0.006 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.28 (36034) covalent geometry : angle 1.14406 / 0.46 (53892) hydrogen bonds : bond 0.06675 / 3.42 ( 1427) hydrogen bonds : angle 2.94962 / 1.19 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: e 208 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6081 (mtpp) REVERT: f 53 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (tpp80) REVERT: f 74 ASP cc_start: 0.6915 (t70) cc_final: 0.6573 (t70) REVERT: g 31 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: g 96 ILE cc_start: 0.8436 (mm) cc_final: 0.7807 (mp) REVERT: i 70 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7709 (ptpp) REVERT: l 104 TYR cc_start: 0.7535 (m-80) cc_final: 0.7096 (m-80) REVERT: m 43 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7973 (mtpp) REVERT: m 86 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8345 (ppt-90) REVERT: q 48 GLU cc_start: 0.7697 (tt0) cc_final: 0.7388 (tt0) REVERT: r 20 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8452 (ptmt) REVERT: s 35 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: v 46 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7366 (mtmt) outliers start: 59 outliers final: 38 residues processed: 287 average time/residue: 0.8009 time to fit residues: 269.7732 Evaluate side-chains 294 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain v residue 46 LYS Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 214 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 0.0000 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110631 restraints weight = 39447.916| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.35 r_work: 0.3049 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36034 Z= 0.263 Angle : 1.135 19.754 53892 Z= 0.459 Chirality : 0.095 1.148 6919 Planarity : 0.004 0.034 2984 Dihedral : 19.136 179.726 14106 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.61 % Allowed : 29.46 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.16 (0.22), residues: 1470 helix: 1.38 (0.21), residues: 604 sheet: -0.40 (0.33), residues: 256 loop : -1.51 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG s 43 TYR 0.015 0.002 TYR m 117 PHE 0.026 0.002 PHE v 37 TRP 0.009 0.002 TRP l 43 HIS 0.008 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (36034) covalent geometry : angle 1.13506 / 0.46 (53892) hydrogen bonds : bond 0.06638 / 3.40 ( 1427) hydrogen bonds : angle 2.94490 / 1.19 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: e 208 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6092 (mtpp) REVERT: f 53 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7835 (tpp80) REVERT: f 74 ASP cc_start: 0.6899 (t70) cc_final: 0.6559 (t70) REVERT: g 31 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: g 96 ILE cc_start: 0.8444 (mm) cc_final: 0.8202 (mt) REVERT: i 70 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7697 (ptpp) REVERT: l 104 TYR cc_start: 0.7527 (m-80) cc_final: 0.7087 (m-80) REVERT: m 43 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: m 86 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8366 (ppt-90) REVERT: q 48 GLU cc_start: 0.7719 (tt0) cc_final: 0.7413 (tt0) REVERT: r 20 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8395 (ptmt) REVERT: s 35 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: v 46 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7301 (mtmt) outliers start: 56 outliers final: 39 residues processed: 286 average time/residue: 0.7932 time to fit residues: 266.5876 Evaluate side-chains 296 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain v residue 46 LYS Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 218 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN i 41 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110015 restraints weight = 39612.847| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.37 r_work: 0.3044 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.2805 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 36034 Z= 0.254 Angle : 1.128 19.663 53892 Z= 0.457 Chirality : 0.094 1.143 6919 Planarity : 0.005 0.089 2984 Dihedral : 19.144 179.892 14106 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.91 % Allowed : 30.46 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.13 (0.22), residues: 1470 helix: 1.41 (0.21), residues: 604 sheet: -0.38 (0.33), residues: 256 loop : -1.51 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG f 111 TYR 0.014 0.002 TYR m 117 PHE 0.022 0.002 PHE v 37 TRP 0.009 0.002 TRP l 43 HIS 0.007 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.25 (36034) covalent geometry : angle 1.12777 / 0.46 (53892) hydrogen bonds : bond 0.06620 / 3.39 ( 1427) hydrogen bonds : angle 2.93639 / 1.18 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: e 208 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6131 (mtpp) REVERT: f 74 ASP cc_start: 0.6978 (t70) cc_final: 0.6641 (t70) REVERT: g 31 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: g 71 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8003 (tm) REVERT: g 96 ILE cc_start: 0.8456 (mm) cc_final: 0.8208 (mt) REVERT: i 70 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7736 (ptpp) REVERT: l 104 TYR cc_start: 0.7537 (m-80) cc_final: 0.7085 (m-80) REVERT: m 43 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8026 (mtpp) REVERT: m 86 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8427 (ppt-90) REVERT: q 48 GLU cc_start: 0.7857 (tt0) cc_final: 0.7552 (tt0) REVERT: r 20 LYS cc_start: 0.8723 (ptpt) cc_final: 0.8427 (ptmt) REVERT: s 35 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: v 46 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7487 (mtmt) outliers start: 49 outliers final: 37 residues processed: 282 average time/residue: 0.7718 time to fit residues: 256.2925 Evaluate side-chains 295 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain v residue 46 LYS Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 242 optimal weight: 0.0070 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 41 GLN e 42 HIS e 177 HIS g 52 ASN i 41 GLN l 107 ASN m 111 ASN p 20 ASN p 37 ASN p 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111485 restraints weight = 39355.103| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.33 r_work: 0.3057 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36034 Z= 0.217 Angle : 1.113 19.635 53892 Z= 0.451 Chirality : 0.093 1.138 6919 Planarity : 0.004 0.079 2984 Dihedral : 19.156 179.868 14106 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.01 % Allowed : 30.26 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.22), residues: 1470 helix: 1.44 (0.21), residues: 605 sheet: -0.33 (0.35), residues: 235 loop : -1.45 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG f 111 TYR 0.014 0.002 TYR m 117 PHE 0.022 0.002 PHE v 37 TRP 0.009 0.002 TRP l 43 HIS 0.007 0.001 HIS e 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (36034) covalent geometry : angle 1.11305 / 0.45 (53892) hydrogen bonds : bond 0.06595 / 3.38 ( 1427) hydrogen bonds : angle 2.92869 / 1.18 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12792.62 seconds wall clock time: 218 minutes 19.47 seconds (13099.47 seconds total)