Starting phenix.real_space_refine on Tue Aug 26 01:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yt9_10914/08_2025/6yt9_10914.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yt9_10914/08_2025/6yt9_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_10914/08_2025/6yt9_10914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yt9_10914/08_2025/6yt9_10914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yt9_10914/08_2025/6yt9_10914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yt9_10914/08_2025/6yt9_10914.map" } 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-2.0-5787/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 7.77, per 1000 atoms: 0.23 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: 3.52 Conformation dependent library (CDL) restraints added in 739.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 5.89 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: 14.33 Time building geometry restraints manager: 3.70 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=" C3' C 2 99 " pdb=" C2' C 2 99 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.50e-02 4.44e+03 3.29e+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 bond pdb=" C8 G 2 100 " pdb=" N7 G 2 100 " ideal model delta sigma weight residual 1.305 1.272 0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 36029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 51232 1.67 - 3.35: 2382 3.35 - 5.02: 235 5.02 - 6.69: 38 6.69 - 8.36: 5 Bond angle restraints: 53892 Sorted by residual: angle pdb=" C2' G 2 100 " pdb=" C1' G 2 100 " pdb=" N9 G 2 100 " ideal model delta sigma weight residual 112.00 103.64 8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C2' C 2 99 " pdb=" C1' C 2 99 " pdb=" N1 C 2 99 " ideal model delta sigma weight residual 114.00 107.05 6.95 1.50e+00 4.44e-01 2.15e+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=" 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=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.03 -5.83 1.50e+00 4.44e-01 1.51e+01 ... (remaining 53887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 20057 35.68 - 71.36: 2626 71.36 - 107.05: 270 107.05 - 142.73: 4 142.73 - 178.41: 7 Dihedral angle restraints: 22964 sinusoidal: 18678 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 172 " pdb=" C1' C 2 172 " pdb=" N1 C 2 172 " pdb=" C2 C 2 172 " ideal model delta sinusoidal sigma weight residual -160.00 18.41 -178.41 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 435 " pdb=" C1' U 2 435 " pdb=" N1 U 2 435 " pdb=" C2 U 2 435 " ideal model delta sinusoidal sigma weight residual -160.00 -10.94 -149.06 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' U 2 419 " pdb=" C1' U 2 419 " pdb=" N1 U 2 419 " pdb=" C2 U 2 419 " ideal model delta sinusoidal sigma weight residual 200.00 55.66 144.34 1 1.50e+01 4.44e-03 7.73e+01 ... (remaining 22961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 6252 0.080 - 0.161: 621 0.161 - 0.241: 42 0.241 - 0.321: 3 0.321 - 0.401: 1 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 -2.75 -2.35 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1' A 2 5 " pdb=" O4' A 2 5 " pdb=" C2' A 2 5 " pdb=" N9 A 2 5 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1' A 2 294 " pdb=" O4' A 2 294 " pdb=" C2' A 2 294 " pdb=" N9 A 2 294 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.55e+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: 4.390 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 42.070 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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= 0.499 Angle : 0.807 8.363 53892 Z= 0.421 Chirality : 0.049 0.401 6919 Planarity : 0.006 0.046 2984 Dihedral : 23.865 178.410 20198 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 aren 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 covalent geometry : bond 0.00972 (36034) covalent geometry : angle 0.80685 (53892) hydrogen bonds : bond 0.11707 ( 1427) hydrogen bonds : angle 4.49766 ( 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 : 0.689 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: 0.8670 time to fit residues: 315.5533 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 : 0.704 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 46 HIS p 62 GLN q 44 GLN q 46 GLN u 6 GLN v 57 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111970 restraints weight = 39422.034| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.30 r_work: 0.3033 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work: 0.2814 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36034 Z= 0.174 Angle : 0.570 6.486 53892 Z= 0.300 Chirality : 0.036 0.209 6919 Planarity : 0.004 0.038 2984 Dihedral : 23.620 175.757 17915 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.11 % Allowed : 25.15 % Favored : 69.74 % 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 aren not related in a simple way. whole: -1.82 (0.20), residues: 1470 helix: -0.12 (0.20), residues: 613 sheet: -1.28 (0.30), residues: 254 loop : -2.28 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 24 TYR 0.011 0.001 TYR m 117 PHE 0.013 0.001 PHE e 184 TRP 0.009 0.001 TRP q 60 HIS 0.003 0.001 HIS g 58 Details of bonding type rmsd covalent geometry : bond 0.00328 (36034) covalent geometry : angle 0.56979 (53892) hydrogen bonds : bond 0.06114 ( 1427) hydrogen bonds : angle 3.23950 ( 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 314 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7841 (p-80) REVERT: e 130 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7049 (ttm170) REVERT: e 167 ARG cc_start: 0.5739 (tmm160) cc_final: 0.5313 (ttp-170) REVERT: g 14 GLN cc_start: 0.7794 (mp-120) cc_final: 0.7449 (mm110) REVERT: g 63 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8620 (m110) REVERT: g 68 GLN cc_start: 0.7818 (tp40) cc_final: 0.7604 (tp-100) REVERT: g 96 ILE cc_start: 0.8468 (mm) cc_final: 0.8155 (mt) REVERT: l 104 TYR cc_start: 0.7462 (m-80) cc_final: 0.7115 (m-80) REVERT: m 86 ARG cc_start: 0.8816 (ptt180) cc_final: 0.8352 (ppt-90) REVERT: m 88 LYS cc_start: 0.8707 (tptp) cc_final: 0.8487 (ttmm) REVERT: p 22 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8363 (m) REVERT: q 48 GLU cc_start: 0.7982 (tt0) cc_final: 0.7721 (tt0) REVERT: r 20 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8268 (pttt) REVERT: s 35 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7666 (pt0) outliers start: 51 outliers final: 24 residues processed: 303 average time/residue: 0.8546 time to fit residues: 301.3829 Evaluate side-chains 279 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 l residue 15 VAL Chi-restraints excluded: chain l residue 41 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 47 SER 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 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: 5.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 28 GLN g 52 ASN i 41 GLN i 42 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 37 ASN p 62 GLN p 75 HIS q 46 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 = 0.3472 r_free = 0.3472 target = 0.123984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102318 restraints weight = 39457.196| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.43 r_work: 0.2897 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work: 0.2655 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 36034 Z= 0.444 Angle : 0.752 7.620 53892 Z= 0.381 Chirality : 0.046 0.247 6919 Planarity : 0.006 0.049 2984 Dihedral : 23.654 178.660 17863 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 7.21 % Allowed : 25.35 % Favored : 67.43 % 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 aren not related in a simple way. whole: -1.48 (0.21), residues: 1470 helix: 0.22 (0.21), residues: 609 sheet: -1.05 (0.31), residues: 259 loop : -2.20 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 9 TYR 0.021 0.002 TYR m 117 PHE 0.022 0.003 PHE e 184 TRP 0.010 0.002 TRP r 74 HIS 0.005 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00868 (36034) covalent geometry : angle 0.75186 (53892) hydrogen bonds : bond 0.07370 ( 1427) hydrogen bonds : angle 3.28293 ( 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 321 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 249 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8047 (p-80) REVERT: e 130 ARG cc_start: 0.7381 (mtp180) cc_final: 0.7007 (ttm170) REVERT: e 167 ARG cc_start: 0.5691 (tmm160) cc_final: 0.5334 (ttp-170) REVERT: f 40 ASP cc_start: 0.8527 (p0) cc_final: 0.8301 (p0) REVERT: f 53 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7869 (tpp80) REVERT: g 31 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: g 68 GLN cc_start: 0.7965 (tp40) cc_final: 0.7733 (tp-100) REVERT: g 71 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8016 (tm) REVERT: g 96 ILE cc_start: 0.8184 (mm) cc_final: 0.7906 (mt) REVERT: l 56 LYS cc_start: 0.8091 (pttt) cc_final: 0.7877 (ttpt) REVERT: l 104 TYR cc_start: 0.7554 (m-80) cc_final: 0.7167 (m-80) REVERT: m 43 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8017 (mtpp) REVERT: m 86 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8177 (ppt-90) REVERT: m 88 LYS cc_start: 0.8749 (tptp) cc_final: 0.8457 (ttmm) REVERT: p 22 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8309 (m) REVERT: q 48 GLU cc_start: 0.7760 (tt0) cc_final: 0.7500 (tt0) REVERT: r 20 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8294 (pttt) REVERT: r 30 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7909 (m) REVERT: s 35 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7740 (pt0) outliers start: 72 outliers final: 41 residues processed: 296 average time/residue: 0.8527 time to fit residues: 293.9758 Evaluate side-chains 294 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 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 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 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 s residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 237 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 182 optimal weight: 0.0030 chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 91 ASN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 42 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN p 62 GLN p 75 HIS q 46 GLN v 57 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104686 restraints weight = 39220.402| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.36 r_work: 0.2962 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 36034 Z= 0.203 Angle : 0.574 6.657 53892 Z= 0.301 Chirality : 0.037 0.204 6919 Planarity : 0.004 0.039 2984 Dihedral : 23.511 175.332 17863 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 6.11 % Allowed : 26.55 % Favored : 67.33 % 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 aren not related in a simple way. whole: -0.89 (0.21), residues: 1470 helix: 0.74 (0.21), residues: 612 sheet: -0.79 (0.32), residues: 261 loop : -1.92 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 24 TYR 0.015 0.002 TYR m 117 PHE 0.015 0.002 PHE v 37 TRP 0.010 0.001 TRP q 60 HIS 0.002 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00388 (36034) covalent geometry : angle 0.57445 (53892) hydrogen bonds : bond 0.06000 ( 1427) hydrogen bonds : angle 3.03360 ( 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 323 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7812 (p-80) REVERT: e 130 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6883 (ttm170) REVERT: e 167 ARG cc_start: 0.5444 (tmm160) cc_final: 0.5111 (ttp-170) REVERT: f 40 ASP cc_start: 0.8625 (p0) cc_final: 0.8381 (p0) REVERT: f 53 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7782 (tpp80) REVERT: g 14 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7489 (mm110) REVERT: g 71 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7998 (tm) REVERT: g 96 ILE cc_start: 0.8428 (mm) cc_final: 0.7857 (mp) REVERT: l 104 TYR cc_start: 0.7504 (m-80) cc_final: 0.7085 (m-80) REVERT: m 43 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7919 (mtpp) REVERT: m 86 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8328 (ppt-90) REVERT: q 48 GLU cc_start: 0.7679 (tt0) cc_final: 0.7394 (tt0) REVERT: r 20 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8291 (pttt) outliers start: 61 outliers final: 34 residues processed: 306 average time/residue: 0.8076 time to fit residues: 287.4746 Evaluate side-chains 293 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 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 108 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 78 LEU Chi-restraints excluded: chain l residue 96 VAL 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 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 14 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 168 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 103 optimal weight: 0.0030 chunk 124 optimal weight: 0.0070 chunk 208 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 0.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 28 GLN g 52 ASN g 63 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 37 ASN p 62 GLN q 46 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 = 0.3540 r_free = 0.3540 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107859 restraints weight = 39390.926| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 0.31 r_work: 0.2995 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36034 Z= 0.145 Angle : 0.551 7.711 53892 Z= 0.290 Chirality : 0.035 0.198 6919 Planarity : 0.004 0.040 2984 Dihedral : 23.503 174.613 17856 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.61 % Allowed : 28.36 % 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 aren not related in a simple way. whole: -0.59 (0.22), residues: 1470 helix: 1.04 (0.22), residues: 606 sheet: -0.65 (0.33), residues: 261 loop : -1.77 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG r 41 TYR 0.013 0.001 TYR m 117 PHE 0.017 0.002 PHE v 37 TRP 0.009 0.001 TRP q 60 HIS 0.002 0.001 HIS g 58 Details of bonding type rmsd covalent geometry : bond 0.00273 (36034) covalent geometry : angle 0.55070 (53892) hydrogen bonds : bond 0.05789 ( 1427) hydrogen bonds : angle 2.98050 ( 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 313 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7790 (p-80) REVERT: e 130 ARG cc_start: 0.7212 (mtp180) cc_final: 0.6929 (ttm170) REVERT: f 53 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7741 (tpp80) REVERT: g 96 ILE cc_start: 0.8402 (mm) cc_final: 0.8169 (mt) REVERT: i 70 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7723 (ptpp) REVERT: l 104 TYR cc_start: 0.7493 (m-80) cc_final: 0.7117 (m-80) REVERT: m 43 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7905 (mtpp) REVERT: m 86 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8331 (ppt-90) REVERT: q 48 GLU cc_start: 0.7653 (tt0) cc_final: 0.7375 (tt0) REVERT: r 20 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8289 (pttt) REVERT: s 35 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7546 (pt0) outliers start: 56 outliers final: 35 residues processed: 294 average time/residue: 0.8118 time to fit residues: 277.3489 Evaluate side-chains 285 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 42 HIS 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 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 70 THR 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 15 LEU Chi-restraints excluded: chain m residue 21 VAL 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 p residue 20 ASN Chi-restraints excluded: chain p residue 54 ARG 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 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 144 optimal weight: 0.0670 chunk 42 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 52 ASN g 63 ASN i 41 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108615 restraints weight = 39391.654| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.31 r_work: 0.3003 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36034 Z= 0.153 Angle : 0.530 7.399 53892 Z= 0.278 Chirality : 0.034 0.188 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.355 174.851 17855 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.81 % Allowed : 28.16 % 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 aren not related in a simple way. whole: -0.20 (0.22), residues: 1470 helix: 1.35 (0.22), residues: 606 sheet: -0.40 (0.34), residues: 252 loop : -1.55 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 44 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 0.002 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00291 (36034) covalent geometry : angle 0.53036 (53892) hydrogen bonds : bond 0.05496 ( 1427) hydrogen bonds : angle 2.85690 ( 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 317 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7734 (p-80) REVERT: e 130 ARG cc_start: 0.7214 (mtp180) cc_final: 0.6941 (ttm170) REVERT: f 74 ASP cc_start: 0.6950 (t70) cc_final: 0.6621 (t70) REVERT: g 31 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: g 70 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8344 (m) REVERT: g 96 ILE cc_start: 0.8433 (mm) cc_final: 0.8201 (mt) REVERT: i 70 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7700 (ptpp) REVERT: l 104 TYR cc_start: 0.7528 (m-80) cc_final: 0.7058 (m-80) REVERT: m 40 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8290 (p) REVERT: m 43 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7864 (mtpp) REVERT: m 47 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8175 (p) REVERT: m 86 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8355 (ppt-90) REVERT: q 48 GLU cc_start: 0.7695 (tt0) cc_final: 0.7411 (tt0) REVERT: r 20 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8332 (ptmt) REVERT: r 28 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5852 (ptm-80) REVERT: s 35 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: u 37 SER cc_start: 0.8934 (p) cc_final: 0.8726 (m) outliers start: 58 outliers final: 29 residues processed: 294 average time/residue: 0.8405 time to fit residues: 288.1404 Evaluate side-chains 288 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 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 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 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 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 54 ARG 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 28 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 48 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3518 r_free = 0.3518 target = 0.127423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105056 restraints weight = 39414.299| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.37 r_work: 0.2952 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1355 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= 0.244 Angle : 0.589 7.552 53892 Z= 0.306 Chirality : 0.037 0.209 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.374 176.385 17854 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.91 % Allowed : 28.26 % Favored : 65.83 % 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 aren not related in a simple way. whole: -0.24 (0.22), residues: 1470 helix: 1.28 (0.21), residues: 606 sheet: -0.37 (0.34), residues: 254 loop : -1.57 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 13 TYR 0.015 0.002 TYR m 117 PHE 0.019 0.002 PHE v 37 TRP 0.008 0.002 TRP q 60 HIS 0.003 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00472 (36034) covalent geometry : angle 0.58927 (53892) hydrogen bonds : bond 0.05984 ( 1427) hydrogen bonds : angle 2.91306 ( 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 305 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7809 (p-80) REVERT: f 53 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7838 (tpp80) REVERT: g 31 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: g 70 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8350 (m) REVERT: g 96 ILE cc_start: 0.8460 (mm) cc_final: 0.8224 (mt) REVERT: i 70 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7732 (ptpp) REVERT: l 104 TYR cc_start: 0.7579 (m-80) cc_final: 0.7145 (m-80) REVERT: m 43 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7934 (mtpp) REVERT: m 86 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8325 (ppt-90) REVERT: q 48 GLU cc_start: 0.7733 (tt0) cc_final: 0.7453 (tt0) REVERT: r 20 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8401 (ptmt) REVERT: r 28 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.5688 (ptm-80) REVERT: s 35 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: u 37 SER cc_start: 0.8993 (p) cc_final: 0.8737 (m) outliers start: 59 outliers final: 35 residues processed: 285 average time/residue: 0.7585 time to fit residues: 251.3939 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 : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 53 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 161 GLU 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 34 THR Chi-restraints excluded: chain l residue 41 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 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 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 54 ARG 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 28 ARG Chi-restraints excluded: chain r residue 66 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 98 GLN ** l 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3481 r_free = 0.3481 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102712 restraints weight = 39285.014| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.42 r_work: 0.2908 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 36034 Z= 0.392 Angle : 0.714 8.359 53892 Z= 0.364 Chirality : 0.044 0.232 6919 Planarity : 0.005 0.046 2984 Dihedral : 23.520 178.228 17854 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.71 % Allowed : 28.46 % Favored : 64.83 % 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 aren not related in a simple way. whole: -0.57 (0.21), residues: 1470 helix: 0.95 (0.21), residues: 611 sheet: -0.47 (0.33), residues: 254 loop : -1.74 (0.23), residues: 605 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 0.024 0.003 PHE e 184 TRP 0.011 0.002 TRP r 74 HIS 0.005 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00766 (36034) covalent geometry : angle 0.71407 (53892) hydrogen bonds : bond 0.07120 ( 1427) hydrogen bonds : angle 3.09306 ( 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 317 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7375 (p-80) REVERT: e 117 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7675 (ttt90) REVERT: e 167 ARG cc_start: 0.5528 (tmm160) cc_final: 0.5069 (ttp-170) REVERT: f 53 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7892 (tpp80) REVERT: g 31 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: g 96 ILE cc_start: 0.8459 (mm) cc_final: 0.7825 (mp) REVERT: l 104 TYR cc_start: 0.7594 (m-80) cc_final: 0.7156 (m-80) REVERT: m 43 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8031 (mtpp) REVERT: m 86 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8271 (ppt-90) REVERT: q 48 GLU cc_start: 0.7714 (tt0) cc_final: 0.7398 (tt0) REVERT: r 20 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8253 (pttt) REVERT: r 28 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.5285 (ptm-80) REVERT: s 35 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7513 (pt0) outliers start: 67 outliers final: 41 residues processed: 291 average time/residue: 0.8410 time to fit residues: 284.6698 Evaluate side-chains 294 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 117 ARG 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 31 GLU Chi-restraints excluded: chain g residue 54 ILE 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 34 THR Chi-restraints excluded: chain l residue 41 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 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 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 54 ARG 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 28 ARG 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 s residue 47 THR Chi-restraints excluded: chain u residue 27 MET Chi-restraints excluded: chain u residue 30 THR 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: 0.7980 chunk 187 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106534 restraints weight = 39447.650| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.35 r_work: 0.2991 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36034 Z= 0.151 Angle : 0.552 8.081 53892 Z= 0.289 Chirality : 0.035 0.202 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.423 174.751 17854 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.01 % Allowed : 29.96 % Favored : 65.03 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1470 helix: 1.32 (0.21), residues: 607 sheet: -0.35 (0.35), residues: 235 loop : -1.46 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG r 28 TYR 0.013 0.001 TYR m 117 PHE 0.022 0.001 PHE v 37 TRP 0.010 0.001 TRP q 60 HIS 0.002 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00286 (36034) covalent geometry : angle 0.55150 (53892) hydrogen bonds : bond 0.05705 ( 1427) hydrogen bonds : angle 2.89793 ( 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 312 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7710 (p-80) REVERT: g 31 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: g 70 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8309 (m) REVERT: g 96 ILE cc_start: 0.8435 (mm) cc_final: 0.8187 (mt) REVERT: i 70 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7718 (ptpp) REVERT: l 104 TYR cc_start: 0.7521 (m-80) cc_final: 0.7124 (m-80) REVERT: m 43 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7838 (mtpp) REVERT: m 86 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8320 (ppt-90) REVERT: q 48 GLU cc_start: 0.7627 (tt0) cc_final: 0.7328 (tt0) REVERT: r 20 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8331 (ptmt) REVERT: s 35 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: u 37 SER cc_start: 0.8890 (p) cc_final: 0.8669 (m) outliers start: 50 outliers final: 31 residues processed: 296 average time/residue: 0.8704 time to fit residues: 299.9361 Evaluate side-chains 292 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 g residue 31 GLU 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 70 LYS 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 l residue 106 ILE 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 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 55 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 218 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 177 HIS g 52 ASN g 63 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3517 r_free = 0.3517 target = 0.127336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106057 restraints weight = 39450.249| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.34 r_work: 0.2958 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work: 0.2705 rms_B_bonded: 4.86 restraints_weight: 0.1250 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 36034 Z= 0.241 Angle : 0.594 8.465 53892 Z= 0.309 Chirality : 0.037 0.208 6919 Planarity : 0.004 0.035 2984 Dihedral : 23.387 176.060 17854 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.41 % Allowed : 30.66 % 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 aren not related in a simple way. whole: -0.20 (0.22), residues: 1470 helix: 1.31 (0.21), residues: 606 sheet: -0.40 (0.33), residues: 256 loop : -1.52 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG s 43 TYR 0.015 0.002 TYR v 38 PHE 0.023 0.002 PHE v 37 TRP 0.007 0.002 TRP q 60 HIS 0.003 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00465 (36034) covalent geometry : angle 0.59408 (53892) hydrogen bonds : bond 0.06004 ( 1427) hydrogen bonds : angle 2.93147 ( 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 292 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7413 (p-80) REVERT: g 31 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: g 70 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8369 (m) REVERT: g 96 ILE cc_start: 0.8490 (mm) cc_final: 0.8239 (mt) REVERT: l 104 TYR cc_start: 0.7567 (m-80) cc_final: 0.7166 (m-80) REVERT: m 43 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8009 (mtpp) REVERT: m 86 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8455 (ppt-90) REVERT: q 48 GLU cc_start: 0.7844 (tt0) cc_final: 0.7531 (tt0) REVERT: r 20 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8366 (ptmt) REVERT: r 28 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.5585 (ptm-80) REVERT: s 35 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: u 37 SER cc_start: 0.8949 (p) cc_final: 0.8718 (m) outliers start: 44 outliers final: 32 residues processed: 278 average time/residue: 0.9010 time to fit residues: 290.9740 Evaluate side-chains 286 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 42 HIS 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 g residue 31 GLU 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 l residue 34 THR Chi-restraints excluded: chain l residue 41 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 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 54 ARG 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 28 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 242 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 52 ASN g 63 ASN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 37 ASN p 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106081 restraints weight = 39152.471| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.32 r_work: 0.2970 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36034 Z= 0.189 Angle : 0.580 8.462 53892 Z= 0.303 Chirality : 0.036 0.202 6919 Planarity : 0.004 0.035 2984 Dihedral : 23.392 175.780 17854 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.41 % Allowed : 30.96 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1470 helix: 1.35 (0.21), residues: 606 sheet: -0.40 (0.33), residues: 256 loop : -1.50 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG s 43 TYR 0.015 0.002 TYR m 117 PHE 0.023 0.002 PHE v 37 TRP 0.009 0.001 TRP q 60 HIS 0.003 0.001 HIS f 88 Details of bonding type rmsd covalent geometry : bond 0.00363 (36034) covalent geometry : angle 0.57970 (53892) hydrogen bonds : bond 0.05954 ( 1427) hydrogen bonds : angle 2.92075 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13350.99 seconds wall clock time: 228 minutes 6.09 seconds (13686.09 seconds total)