Starting phenix.real_space_refine on Sun Sep 13 19:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zol_11322/09_2026/6zol_11322.map" } resolution = 2.8 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= -0.002 sd= 0.125 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 472 5.49 5 Mg 57 5.21 5 S 77 5.16 5 C 14250 2.51 5 N 4678 2.21 5 O 6055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25591 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 10050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 10050 Classifications: {'RNAv2': 472} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 41, 'rna3p_pur': 192, 'rna3p_pyr': 195} Link IDs: {'rna2p': 85, 'rna3p': 386} Chain breaks: 1 Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "F" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1501 Classifications: {'peptide': 190} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "R" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 671 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 95} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "2" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 53} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22215 SG CYS d 21 84.334 85.654 49.120 1.00 16.22 S ATOM 22239 SG CYS d 24 83.484 86.587 45.608 1.00 16.50 S ATOM 22360 SG CYS d 39 86.884 85.363 46.355 1.00 15.00 S ATOM 22386 SG CYS d 42 86.115 88.637 47.499 1.00 14.69 S ATOM 22880 SG CYS f 121 37.860 67.544 58.710 1.00 66.69 S ATOM 22916 SG CYS f 126 39.604 71.000 58.991 1.00 69.25 S ATOM 23034 SG CYS f 141 38.561 69.510 55.564 1.00 55.42 S ATOM 23053 SG CYS f 144 41.401 68.082 57.473 1.00 57.69 S Time building chain proxies: 4.73, per 1000 atoms: 0.18 Number of scatterers: 25591 At special positions: 0 Unit cell: (181.44, 140.4, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 77 16.00 P 472 15.00 Mg 57 11.99 O 6055 8.00 N 4678 7.00 C 14250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 814.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " Number of angles added : 12 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 26 sheets defined 41.0% alpha, 20.2% beta 125 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'D' and resid 6 through 30 Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.338A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.668A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.644A pdb=" N LEU D 96 " --> pdb=" O THR D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.560A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 4.211A pdb=" N TYR D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 33 through 38 removed outlier: 4.246A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 67 through 76 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.576A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.541A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 163 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.562A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 removed outlier: 3.512A pdb=" N ARG K 55 " --> pdb=" O SER K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'M' and resid 17 through 28 removed outlier: 4.164A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 58 through 72 Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 117 through 132 removed outlier: 3.515A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.877A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.546A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.644A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.614A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.719A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.955A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 100 removed outlier: 3.528A pdb=" N GLN Q 86 " --> pdb=" O TYR Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.681A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.666A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'R' and resid 71 through 82 Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.619A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) 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 37 through 48 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.811A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.529A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.503A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.790A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.886A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.553A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 145 Processing helix chain 'U' and resid 28 through 46 removed outlier: 3.652A pdb=" N LEU U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 105 removed outlier: 3.666A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.581A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 104 No H-bonds generated for 'chain 'f' and resid 102 through 104' Processing helix chain 'g' and resid 276 through 280 removed outlier: 3.794A pdb=" N LYS g 280 " --> pdb=" O THR g 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 34 through 41 removed outlier: 6.645A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 85 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.774A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.508A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 223 through 226 removed outlier: 6.439A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 123 through 129 removed outlier: 25.517A pdb=" N ILE c 43 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 18.063A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 13.486A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS c 27 " --> pdb=" O ARG c 20 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG c 20 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS c 16 " --> pdb=" O ARG c 31 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU c 33 " --> pdb=" O VAL c 14 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL c 14 " --> pdb=" O GLU c 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.707A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 92 through 93 removed outlier: 4.503A pdb=" N LYS M 102 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AB1, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AB2, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id=AB3, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AB4, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.912A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'U' and resid 50 through 55 removed outlier: 5.831A pdb=" N LEU U 88 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG U 55 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS U 86 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 59 through 66 removed outlier: 8.940A pdb=" N ARG U 79 " --> pdb=" O LEU d 55 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU d 55 " --> pdb=" O ARG U 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.846A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AC1, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AC2, first strand: chain 'f' and resid 133 through 135 removed outlier: 3.502A pdb=" N ARG f 138 " --> pdb=" O HIS f 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 3 through 11 removed outlier: 5.418A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 18 through 22 removed outlier: 3.582A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.558A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.511A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.136A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA g 216 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR g 229 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS g 225 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.814A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE g 265 " --> pdb=" O ASP g 260 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5181 1.33 - 1.45: 8262 1.45 - 1.57: 12472 1.57 - 1.69: 942 1.69 - 1.81: 115 Bond restraints: 26972 Sorted by residual: bond pdb=" N LYS Q 17 " pdb=" CA LYS Q 17 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.17e-02 7.31e+03 4.18e+00 bond pdb=" N ALA S 100 " pdb=" CA ALA S 100 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.15e+00 bond pdb=" N ALA F 131 " pdb=" CA ALA F 131 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.04e+00 bond pdb=" N ARG M 45 " pdb=" CA ARG M 45 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CA SER F 75 " pdb=" C SER F 75 " ideal model delta sigma weight residual 1.522 1.508 0.015 1.37e-02 5.33e+03 1.16e+00 ... (remaining 26967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 36381 1.57 - 3.14: 1756 3.14 - 4.71: 418 4.71 - 6.27: 91 6.27 - 7.84: 2 Bond angle restraints: 38648 Sorted by residual: angle pdb=" N SER U 93 " pdb=" CA SER U 93 " pdb=" C SER U 93 " ideal model delta sigma weight residual 108.22 111.90 -3.68 9.00e-01 1.23e+00 1.67e+01 angle pdb=" N VAL F 41 " pdb=" CA VAL F 41 " pdb=" C VAL F 41 " ideal model delta sigma weight residual 113.20 109.76 3.44 9.60e-01 1.09e+00 1.28e+01 angle pdb=" C ALA Q 122 " pdb=" N ASP Q 123 " pdb=" CA ASP Q 123 " ideal model delta sigma weight residual 121.61 126.04 -4.43 1.39e+00 5.18e-01 1.02e+01 angle pdb=" N LYS Q 16 " pdb=" CA LYS Q 16 " pdb=" C LYS Q 16 " ideal model delta sigma weight residual 109.18 104.74 4.44 1.42e+00 4.96e-01 9.78e+00 angle pdb=" N TRP K 64 " pdb=" CA TRP K 64 " pdb=" CB TRP K 64 " ideal model delta sigma weight residual 110.49 105.67 4.82 1.69e+00 3.50e-01 8.12e+00 ... (remaining 38643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13113 17.92 - 35.84: 1178 35.84 - 53.76: 587 53.76 - 71.69: 427 71.69 - 89.61: 51 Dihedral angle restraints: 15356 sinusoidal: 9769 harmonic: 5587 Sorted by residual: dihedral pdb=" C4' A 21663 " pdb=" C3' A 21663 " pdb=" C2' A 21663 " pdb=" C1' A 21663 " ideal model delta sinusoidal sigma weight residual 36.34 -37.65 73.99 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' G 21330 " pdb=" C3' G 21330 " pdb=" C2' G 21330 " pdb=" C1' G 21330 " ideal model delta sinusoidal sigma weight residual 36.34 -37.51 73.85 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" C2' A 21664 " pdb=" C1' A 21664 " ideal model delta sinusoidal sigma weight residual 36.34 -37.28 73.62 1 3.10e+00 1.04e-01 7.17e+02 ... (remaining 15353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3592 0.061 - 0.122: 438 0.122 - 0.183: 47 0.183 - 0.244: 467 0.244 - 0.304: 170 Chirality restraints: 4714 Sorted by residual: chirality pdb=" C3' A 21663 " pdb=" C4' A 21663 " pdb=" O3' A 21663 " pdb=" C2' A 21663 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C3' A 21664 " pdb=" C4' A 21664 " pdb=" O3' A 21664 " pdb=" C2' A 21664 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' U 21519 " pdb=" C4' U 21519 " pdb=" O3' U 21519 " pdb=" C2' U 21519 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4711 not shown) Planarity restraints: 3154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 21240 " -0.039 2.00e-02 2.50e+03 1.76e-02 8.49e+00 pdb=" N9 A 21240 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A 21240 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A 21240 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 21240 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 21240 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 21240 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A 21240 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 21240 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 21240 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 21240 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21606 " -0.034 2.00e-02 2.50e+03 1.43e-02 6.14e+00 pdb=" N9 G 21606 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G 21606 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 21606 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 21606 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 21606 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 21606 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G 21606 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G 21606 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 21401 " -0.031 2.00e-02 2.50e+03 1.43e-02 5.59e+00 pdb=" N9 A 21401 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A 21401 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 21401 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 21401 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 21401 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 21401 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 21401 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 21401 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 21401 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 21401 " 0.003 2.00e-02 2.50e+03 ... (remaining 3151 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 2 2.03 - 2.75: 2866 2.75 - 3.46: 31887 3.46 - 4.18: 72791 4.18 - 4.90: 110847 Nonbonded interactions: 218393 Sorted by model distance: nonbonded pdb="MG MG 22012 " pdb="MG MG 22042 " model vdw 1.309 1.300 nonbonded pdb=" O6 G 21517 " pdb="MG MG 22001 " model vdw 1.942 2.170 nonbonded pdb=" N4 C 21337 " pdb="MG MG 22015 " model vdw 2.030 2.250 nonbonded pdb=" OP2 C 21262 " pdb="MG MG 22001 " model vdw 2.063 2.170 nonbonded pdb=" OP1 A 21258 " pdb="MG MG 22011 " model vdw 2.074 2.170 ... (remaining 218388 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: 11.380 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26980 Z= 0.163 Angle : 0.816 7.843 38660 Z= 0.370 Chirality : 0.095 0.304 4714 Planarity : 0.004 0.046 3154 Dihedral : 18.781 89.608 11758 Min Nonbonded Distance : 1.309 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.49 % Allowed : 4.18 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1914 helix: 1.82 (0.20), residues: 662 sheet: 0.59 (0.26), residues: 382 loop : -0.66 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 39 TYR 0.014 0.001 TYR F 188 PHE 0.016 0.002 PHE D 79 TRP 0.021 0.002 TRP K 64 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (26972) covalent geometry : angle 0.81446 / 0.37 (38648) hydrogen bonds : bond 0.12639 / 6.62 ( 1019) hydrogen bonds : angle 5.11115 / 2.05 ( 2469) metal coordination : bond 0.04713 / 2.36 ( 8) metal coordination : angle 2.61205 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.738 Fit side-chains REVERT: D 10 LYS cc_start: 0.8231 (tmtp) cc_final: 0.7872 (tttm) REVERT: F 38 TYR cc_start: 0.8760 (m-80) cc_final: 0.8435 (m-80) REVERT: F 78 MET cc_start: 0.8182 (mtt) cc_final: 0.7971 (mtm) REVERT: K 3 MET cc_start: 0.9290 (ptp) cc_final: 0.8641 (ptp) REVERT: K 82 TYR cc_start: 0.8623 (t80) cc_final: 0.8336 (t80) REVERT: P 37 TYR cc_start: 0.9086 (m-10) cc_final: 0.8857 (m-80) REVERT: P 66 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6971 (mt-10) REVERT: S 115 LYS cc_start: 0.8193 (mttt) cc_final: 0.7888 (tmtm) REVERT: T 137 GLN cc_start: 0.8411 (mt0) cc_final: 0.7929 (mt0) REVERT: f 107 LYS cc_start: 0.5806 (pttp) cc_final: 0.5531 (tptm) REVERT: g 165 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7736 (mt) REVERT: g 192 THR cc_start: 0.6744 (m) cc_final: 0.6424 (p) outliers start: 25 outliers final: 9 residues processed: 346 average time/residue: 0.7447 time to fit residues: 294.0681 Evaluate side-chains 257 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 GLN D 179 GLN F 83 ASN F 203 ASN Q 8 GLN Q 114 GLN R 26 ASN T 10 ASN Z 64 ASN c 29 GLN g 215 GLN g 226 HIS g 311 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107669 restraints weight = 29047.912| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 0.71 r_work: 0.2940 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26980 Z= 0.249 Angle : 1.329 18.870 38660 Z= 0.538 Chirality : 0.125 1.264 4714 Planarity : 0.005 0.054 3154 Dihedral : 17.491 154.083 7830 Min Nonbonded Distance : 1.168 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.93 % Allowed : 11.17 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1914 helix: 1.91 (0.20), residues: 670 sheet: 0.63 (0.26), residues: 382 loop : -0.68 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 136 TYR 0.014 0.002 TYR F 188 PHE 0.014 0.002 PHE K 67 TRP 0.015 0.002 TRP g 132 HIS 0.005 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 (26972) covalent geometry : angle 1.32796 / 0.54 (38648) hydrogen bonds : bond 0.05454 / 2.87 ( 1019) hydrogen bonds : angle 4.10532 / 1.67 ( 2469) metal coordination : bond 0.00673 / 0.34 ( 8) metal coordination : angle 3.84924 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.680 Fit side-chains REVERT: D 10 LYS cc_start: 0.8595 (tmtp) cc_final: 0.8238 (tttm) REVERT: F 29 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: F 38 TYR cc_start: 0.8911 (m-80) cc_final: 0.8461 (m-80) REVERT: F 78 MET cc_start: 0.8574 (mtt) cc_final: 0.8331 (mtm) REVERT: F 123 GLU cc_start: 0.8795 (tt0) cc_final: 0.8511 (tt0) REVERT: K 3 MET cc_start: 0.9304 (ptp) cc_final: 0.8728 (ptp) REVERT: K 82 TYR cc_start: 0.8730 (t80) cc_final: 0.8406 (t80) REVERT: P 37 TYR cc_start: 0.9124 (m-10) cc_final: 0.8906 (m-80) REVERT: S 115 LYS cc_start: 0.8449 (mttt) cc_final: 0.8093 (tptp) REVERT: T 10 ASN cc_start: 0.8587 (t0) cc_final: 0.8382 (t0) REVERT: T 137 GLN cc_start: 0.8660 (mt0) cc_final: 0.8190 (mt0) REVERT: c 14 VAL cc_start: 0.9406 (t) cc_final: 0.9154 (t) REVERT: f 107 LYS cc_start: 0.6112 (pttp) cc_final: 0.5329 (tptm) REVERT: g 165 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (mt) REVERT: g 230 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8324 (mm) outliers start: 49 outliers final: 25 residues processed: 285 average time/residue: 0.7016 time to fit residues: 228.5497 Evaluate side-chains 271 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 91 optimal weight: 0.0030 chunk 235 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 114 HIS R 26 ASN U 81 GLN c 29 GLN g 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101856 restraints weight = 29207.900| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 0.88 r_work: 0.2898 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 26980 Z= 0.306 Angle : 1.218 18.320 38660 Z= 0.502 Chirality : 0.110 1.171 4714 Planarity : 0.006 0.057 3154 Dihedral : 17.956 171.091 7829 Min Nonbonded Distance : 1.090 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.94 % Allowed : 12.37 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1914 helix: 1.77 (0.20), residues: 665 sheet: 0.64 (0.27), residues: 374 loop : -0.88 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 121 TYR 0.017 0.002 TYR D 107 PHE 0.015 0.002 PHE Q 132 TRP 0.014 0.002 TRP g 132 HIS 0.006 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (26972) covalent geometry : angle 1.21575 / 0.50 (38648) hydrogen bonds : bond 0.05958 / 3.15 ( 1019) hydrogen bonds : angle 4.08723 / 1.67 ( 2469) metal coordination : bond 0.00647 / 0.32 ( 8) metal coordination : angle 4.36396 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 250 time to evaluate : 0.897 Fit side-chains REVERT: F 29 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: F 78 MET cc_start: 0.8774 (mtt) cc_final: 0.8543 (mtt) REVERT: K 3 MET cc_start: 0.9263 (ptp) cc_final: 0.8634 (ptp) REVERT: K 60 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: K 82 TYR cc_start: 0.8732 (t80) cc_final: 0.8346 (t80) REVERT: M 52 LEU cc_start: 0.7116 (tt) cc_final: 0.6501 (mp) REVERT: R 23 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: S 8 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (mtmt) REVERT: f 107 LYS cc_start: 0.6151 (pttp) cc_final: 0.5385 (tptt) REVERT: g 230 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8317 (mm) REVERT: g 311 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.5063 (tm130) outliers start: 66 outliers final: 35 residues processed: 290 average time/residue: 0.7346 time to fit residues: 243.3589 Evaluate side-chains 271 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain S residue 8 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain g residue 311 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 192 optimal weight: 0.1980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 26 ASN T 12 GLN U 81 GLN c 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103999 restraints weight = 29013.912| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 0.92 r_work: 0.2923 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26980 Z= 0.251 Angle : 1.140 16.368 38660 Z= 0.468 Chirality : 0.101 1.068 4714 Planarity : 0.005 0.059 3154 Dihedral : 17.996 174.394 7827 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.94 % Allowed : 13.62 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1914 helix: 1.81 (0.20), residues: 664 sheet: 0.64 (0.27), residues: 374 loop : -0.91 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 23 TYR 0.017 0.002 TYR D 107 PHE 0.012 0.002 PHE K 67 TRP 0.013 0.002 TRP g 132 HIS 0.006 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (26972) covalent geometry : angle 1.13728 / 0.47 (38648) hydrogen bonds : bond 0.05453 / 2.90 ( 1019) hydrogen bonds : angle 3.99404 / 1.63 ( 2469) metal coordination : bond 0.00476 / 0.24 ( 8) metal coordination : angle 4.19922 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 0.728 Fit side-chains REVERT: F 29 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: F 78 MET cc_start: 0.8681 (mtt) cc_final: 0.8433 (mtt) REVERT: F 122 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7286 (mtm180) REVERT: K 3 MET cc_start: 0.9244 (ptp) cc_final: 0.9030 (ptp) REVERT: K 60 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: K 82 TYR cc_start: 0.8717 (t80) cc_final: 0.8257 (t80) REVERT: S 76 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: c 14 VAL cc_start: 0.9407 (t) cc_final: 0.9176 (t) REVERT: c 33 GLU cc_start: 0.7176 (pp20) cc_final: 0.6942 (pp20) REVERT: f 107 LYS cc_start: 0.6131 (pttp) cc_final: 0.5366 (tptt) REVERT: g 230 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (mm) outliers start: 66 outliers final: 42 residues processed: 275 average time/residue: 0.7238 time to fit residues: 227.7799 Evaluate side-chains 285 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 81 GLN U 92 HIS c 29 GLN g 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107793 restraints weight = 28800.614| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.86 r_work: 0.2968 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26980 Z= 0.187 Angle : 1.035 14.342 38660 Z= 0.423 Chirality : 0.091 0.913 4714 Planarity : 0.005 0.081 3154 Dihedral : 18.025 175.869 7827 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.70 % Allowed : 14.64 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1914 helix: 1.96 (0.20), residues: 666 sheet: 0.71 (0.27), residues: 370 loop : -0.88 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 23 TYR 0.014 0.001 TYR D 107 PHE 0.012 0.001 PHE K 67 TRP 0.014 0.002 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (26972) covalent geometry : angle 1.03329 / 0.42 (38648) hydrogen bonds : bond 0.05019 / 2.68 ( 1019) hydrogen bonds : angle 3.84829 / 1.56 ( 2469) metal coordination : bond 0.00374 / 0.19 ( 8) metal coordination : angle 3.95299 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.755 Fit side-chains REVERT: F 29 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7122 (pp30) REVERT: F 38 TYR cc_start: 0.8919 (m-80) cc_final: 0.8512 (m-80) REVERT: F 78 MET cc_start: 0.8524 (mtt) cc_final: 0.8275 (mtm) REVERT: K 1 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8402 (ttt) REVERT: K 3 MET cc_start: 0.9233 (ptp) cc_final: 0.8554 (ptp) REVERT: K 82 TYR cc_start: 0.8745 (t80) cc_final: 0.8342 (t80) REVERT: P 31 GLU cc_start: 0.8226 (mp0) cc_final: 0.8006 (mp0) REVERT: S 76 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: S 115 LYS cc_start: 0.8518 (mttt) cc_final: 0.8105 (tmtm) REVERT: c 14 VAL cc_start: 0.9412 (t) cc_final: 0.9169 (t) REVERT: f 107 LYS cc_start: 0.5986 (pttp) cc_final: 0.5207 (tptm) REVERT: g 149 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: g 230 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8387 (mm) outliers start: 62 outliers final: 32 residues processed: 289 average time/residue: 0.7290 time to fit residues: 240.9002 Evaluate side-chains 278 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 149 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 73 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 8 GLN U 81 GLN U 92 HIS c 29 GLN g 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110969 restraints weight = 28935.898| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.86 r_work: 0.3028 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26980 Z= 0.152 Angle : 0.966 12.771 38660 Z= 0.394 Chirality : 0.083 0.831 4714 Planarity : 0.004 0.071 3154 Dihedral : 17.930 175.190 7826 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.76 % Allowed : 15.17 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1914 helix: 2.15 (0.20), residues: 660 sheet: 0.78 (0.27), residues: 365 loop : -0.77 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 27 TYR 0.012 0.001 TYR M 61 PHE 0.011 0.001 PHE K 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (26972) covalent geometry : angle 0.96431 / 0.39 (38648) hydrogen bonds : bond 0.04799 / 2.59 ( 1019) hydrogen bonds : angle 3.70984 / 1.50 ( 2469) metal coordination : bond 0.00357 / 0.18 ( 8) metal coordination : angle 3.74430 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 0.787 Fit side-chains REVERT: D 79 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6419 (p90) REVERT: F 29 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7150 (pp30) REVERT: F 38 TYR cc_start: 0.8914 (m-80) cc_final: 0.8502 (m-80) REVERT: F 122 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7226 (mtm180) REVERT: K 1 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8401 (ttt) REVERT: K 3 MET cc_start: 0.9232 (ptp) cc_final: 0.8619 (ptp) REVERT: K 82 TYR cc_start: 0.8699 (t80) cc_final: 0.8406 (t80) REVERT: K 90 VAL cc_start: 0.8171 (m) cc_final: 0.7820 (p) REVERT: P 31 GLU cc_start: 0.8256 (mp0) cc_final: 0.8025 (mp0) REVERT: S 76 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: S 115 LYS cc_start: 0.8465 (mttt) cc_final: 0.8089 (tmtm) REVERT: c 14 VAL cc_start: 0.9463 (t) cc_final: 0.9224 (t) REVERT: f 107 LYS cc_start: 0.5822 (pttp) cc_final: 0.5119 (tptm) REVERT: g 192 THR cc_start: 0.6990 (m) cc_final: 0.6729 (p) outliers start: 63 outliers final: 33 residues processed: 296 average time/residue: 0.7086 time to fit residues: 239.9799 Evaluate side-chains 285 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 34 optimal weight: 4.9990 chunk 205 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 26 ASN U 81 GLN U 92 HIS c 29 GLN g 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109441 restraints weight = 28862.803| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.80 r_work: 0.2997 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26980 Z= 0.179 Angle : 0.997 13.147 38660 Z= 0.408 Chirality : 0.086 0.890 4714 Planarity : 0.005 0.059 3154 Dihedral : 17.885 174.931 7826 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.64 % Allowed : 15.89 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1914 helix: 2.12 (0.20), residues: 660 sheet: 0.61 (0.27), residues: 370 loop : -0.75 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 27 TYR 0.013 0.001 TYR M 61 PHE 0.012 0.001 PHE K 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (26972) covalent geometry : angle 0.99471 / 0.41 (38648) hydrogen bonds : bond 0.04999 / 2.68 ( 1019) hydrogen bonds : angle 3.74108 / 1.51 ( 2469) metal coordination : bond 0.00327 / 0.16 ( 8) metal coordination : angle 3.74465 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.747 Fit side-chains REVERT: D 79 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6500 (p90) REVERT: D 81 GLU cc_start: 0.6623 (mp0) cc_final: 0.6237 (mp0) REVERT: F 29 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7136 (pp30) REVERT: F 38 TYR cc_start: 0.8961 (m-80) cc_final: 0.8556 (m-80) REVERT: F 122 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7270 (mtm180) REVERT: K 1 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8414 (ttt) REVERT: K 3 MET cc_start: 0.9249 (ptp) cc_final: 0.8558 (ptp) REVERT: K 82 TYR cc_start: 0.8700 (t80) cc_final: 0.8378 (t80) REVERT: S 76 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: S 115 LYS cc_start: 0.8498 (mttt) cc_final: 0.8087 (tmtm) REVERT: c 14 VAL cc_start: 0.9437 (t) cc_final: 0.9200 (t) REVERT: f 107 LYS cc_start: 0.5926 (pttp) cc_final: 0.5207 (tptt) REVERT: g 192 THR cc_start: 0.7040 (m) cc_final: 0.6753 (p) REVERT: g 230 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (mm) outliers start: 61 outliers final: 34 residues processed: 288 average time/residue: 0.7054 time to fit residues: 232.0968 Evaluate side-chains 285 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 157 optimal weight: 0.0370 chunk 34 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 26 ASN U 81 GLN U 92 HIS ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109275 restraints weight = 28897.056| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 0.75 r_work: 0.2965 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26980 Z= 0.188 Angle : 1.014 13.731 38660 Z= 0.415 Chirality : 0.088 0.914 4714 Planarity : 0.005 0.058 3154 Dihedral : 17.909 175.023 7826 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 16.37 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1914 helix: 2.09 (0.20), residues: 660 sheet: 0.63 (0.27), residues: 373 loop : -0.72 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 27 TYR 0.014 0.001 TYR D 107 PHE 0.011 0.001 PHE K 67 TRP 0.014 0.001 TRP g 132 HIS 0.005 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (26972) covalent geometry : angle 1.01175 / 0.41 (38648) hydrogen bonds : bond 0.05047 / 2.69 ( 1019) hydrogen bonds : angle 3.75900 / 1.52 ( 2469) metal coordination : bond 0.00335 / 0.17 ( 8) metal coordination : angle 3.71997 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.736 Fit side-chains REVERT: D 79 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6494 (p90) REVERT: D 81 GLU cc_start: 0.6655 (mp0) cc_final: 0.6290 (mp0) REVERT: F 29 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7200 (pp30) REVERT: F 38 TYR cc_start: 0.8969 (m-80) cc_final: 0.8564 (m-80) REVERT: F 122 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7363 (mtm180) REVERT: K 1 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8426 (ttt) REVERT: K 3 MET cc_start: 0.9236 (ptp) cc_final: 0.8555 (ptp) REVERT: K 82 TYR cc_start: 0.8724 (t80) cc_final: 0.8392 (t80) REVERT: M 52 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6577 (mp) REVERT: P 31 GLU cc_start: 0.8231 (mp0) cc_final: 0.8008 (mp0) REVERT: S 76 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: T 8 ASP cc_start: 0.8445 (m-30) cc_final: 0.8220 (m-30) REVERT: c 14 VAL cc_start: 0.9441 (t) cc_final: 0.9201 (t) REVERT: f 107 LYS cc_start: 0.5958 (pttp) cc_final: 0.5231 (tptt) REVERT: g 192 THR cc_start: 0.7094 (m) cc_final: 0.6794 (p) REVERT: g 230 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8405 (mm) outliers start: 60 outliers final: 36 residues processed: 282 average time/residue: 0.7011 time to fit residues: 226.5568 Evaluate side-chains 287 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 4.9990 chunk 157 optimal weight: 0.0470 chunk 202 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 26 ASN U 81 GLN U 92 HIS c 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108396 restraints weight = 28900.724| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.93 r_work: 0.2991 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26980 Z= 0.165 Angle : 0.999 13.408 38660 Z= 0.409 Chirality : 0.086 0.893 4714 Planarity : 0.004 0.057 3154 Dihedral : 17.930 175.205 7826 Min Nonbonded Distance : 1.116 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.52 % Allowed : 16.67 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1914 helix: 2.12 (0.20), residues: 660 sheet: 0.64 (0.27), residues: 373 loop : -0.70 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 50 TYR 0.013 0.001 TYR D 107 PHE 0.011 0.001 PHE K 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (26972) covalent geometry : angle 0.99739 / 0.41 (38648) hydrogen bonds : bond 0.04922 / 2.63 ( 1019) hydrogen bonds : angle 3.74920 / 1.51 ( 2469) metal coordination : bond 0.00327 / 0.16 ( 8) metal coordination : angle 3.65216 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 0.714 Fit side-chains REVERT: D 79 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6461 (p90) REVERT: D 81 GLU cc_start: 0.6588 (mp0) cc_final: 0.6203 (mp0) REVERT: F 29 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7109 (pp30) REVERT: F 38 TYR cc_start: 0.8958 (m-80) cc_final: 0.8547 (m-80) REVERT: F 122 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7315 (mtm180) REVERT: K 1 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8416 (ttt) REVERT: K 3 MET cc_start: 0.9238 (ptp) cc_final: 0.8546 (ptp) REVERT: K 82 TYR cc_start: 0.8690 (t80) cc_final: 0.8344 (t80) REVERT: M 52 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6547 (mp) REVERT: P 31 GLU cc_start: 0.8203 (mp0) cc_final: 0.7991 (mp0) REVERT: S 76 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: T 8 ASP cc_start: 0.8471 (m-30) cc_final: 0.8241 (m-30) REVERT: U 99 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6477 (ptpp) REVERT: c 14 VAL cc_start: 0.9424 (t) cc_final: 0.9189 (t) REVERT: f 107 LYS cc_start: 0.5924 (pttp) cc_final: 0.5217 (tptt) REVERT: g 192 THR cc_start: 0.7043 (m) cc_final: 0.6734 (p) REVERT: g 230 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (mm) outliers start: 59 outliers final: 41 residues processed: 281 average time/residue: 0.7030 time to fit residues: 226.6105 Evaluate side-chains 292 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 99 LYS Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 56 GLN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 8 GLN Q 48 GLN R 26 ASN U 81 GLN U 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101566 restraints weight = 29060.789| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 0.93 r_work: 0.2869 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26980 Z= 0.339 Angle : 1.215 19.008 38660 Z= 0.499 Chirality : 0.108 1.204 4714 Planarity : 0.006 0.062 3154 Dihedral : 18.015 173.279 7826 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.58 % Allowed : 16.61 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1914 helix: 1.77 (0.20), residues: 659 sheet: 0.50 (0.27), residues: 375 loop : -0.87 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 102 TYR 0.019 0.002 TYR D 107 PHE 0.016 0.002 PHE Q 132 TRP 0.013 0.002 TRP g 132 HIS 0.005 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.34 (26972) covalent geometry : angle 1.21331 / 0.50 (38648) hydrogen bonds : bond 0.06144 / 3.24 ( 1019) hydrogen bonds : angle 4.01370 / 1.63 ( 2469) metal coordination : bond 0.00465 / 0.23 ( 8) metal coordination : angle 4.22554 / 1.41 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.769 Fit side-chains REVERT: D 79 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6516 (p90) REVERT: D 81 GLU cc_start: 0.6674 (mp0) cc_final: 0.6325 (mp0) REVERT: F 29 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: F 122 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7428 (mtm180) REVERT: K 1 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8429 (ttt) REVERT: K 3 MET cc_start: 0.9251 (ptp) cc_final: 0.8596 (ptp) REVERT: K 82 TYR cc_start: 0.8791 (t80) cc_final: 0.8365 (t80) REVERT: M 52 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6510 (mp) REVERT: P 71 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7026 (mt-10) REVERT: S 76 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: T 8 ASP cc_start: 0.8583 (m-30) cc_final: 0.8368 (m-30) REVERT: c 14 VAL cc_start: 0.9431 (t) cc_final: 0.9211 (t) REVERT: f 107 LYS cc_start: 0.5983 (pttp) cc_final: 0.5223 (tptt) outliers start: 60 outliers final: 39 residues processed: 284 average time/residue: 0.6460 time to fit residues: 211.2561 Evaluate side-chains 287 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 76 GLN Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 8 GLN U 81 GLN U 92 HIS c 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107702 restraints weight = 29427.001| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.00 r_work: 0.3042 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26980 Z= 0.151 Angle : 0.984 13.080 38660 Z= 0.402 Chirality : 0.084 0.879 4714 Planarity : 0.004 0.064 3154 Dihedral : 18.013 176.282 7826 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.57 % Allowed : 18.04 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1914 helix: 2.06 (0.20), residues: 661 sheet: 0.68 (0.27), residues: 362 loop : -0.74 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 23 TYR 0.013 0.001 TYR M 61 PHE 0.010 0.001 PHE K 67 TRP 0.014 0.001 TRP g 132 HIS 0.003 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (26972) covalent geometry : angle 0.98181 / 0.40 (38648) hydrogen bonds : bond 0.04811 / 2.59 ( 1019) hydrogen bonds : angle 3.75364 / 1.51 ( 2469) metal coordination : bond 0.00339 / 0.17 ( 8) metal coordination : angle 3.53588 / 1.18 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8851.59 seconds wall clock time: 151 minutes 44.21 seconds (9104.21 seconds total)