Starting phenix.real_space_refine on Sat Jun 21 22:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_11322.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_11322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_11322.map" model { file = "/net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_11322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zol_11322/06_2025/6zol_11322.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: 18.03, per 1000 atoms: 0.70 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: 6.24 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 10.22 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: 12.64 Time building geometry restraints manager: 7.55 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: 37860 1.57 - 3.14: 680 3.14 - 4.71: 92 4.71 - 6.27: 14 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=" C2' A 21240 " pdb=" C1' A 21240 " pdb=" N9 A 21240 " ideal model delta sigma weight residual 112.00 116.74 -4.74 1.50e+00 4.44e-01 9.99e+00 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 ... (remaining 38643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 15782 35.94 - 71.88: 1183 71.88 - 107.81: 153 107.81 - 143.75: 2 143.75 - 179.69: 8 Dihedral angle restraints: 17128 sinusoidal: 11541 harmonic: 5587 Sorted by residual: dihedral pdb=" O4' U 21551 " pdb=" C1' U 21551 " pdb=" N1 U 21551 " pdb=" C2 U 21551 " ideal model delta sinusoidal sigma weight residual -160.00 14.51 -174.51 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 4.94 -164.94 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U 21314 " pdb=" C1' U 21314 " pdb=" N1 U 21314 " pdb=" C2 U 21314 " ideal model delta sinusoidal sigma weight residual 200.00 54.28 145.72 1 1.50e+01 4.44e-03 7.79e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3678 0.040 - 0.079: 752 0.079 - 0.119: 235 0.119 - 0.159: 41 0.159 - 0.199: 8 Chirality restraints: 4714 Sorted by residual: chirality pdb=" C1' U 21445 " pdb=" O4' U 21445 " pdb=" C2' U 21445 " pdb=" N1 U 21445 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" C1' A 21240 " pdb=" O4' A 21240 " pdb=" C2' A 21240 " pdb=" N9 A 21240 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" C1' G 21604 " pdb=" O4' G 21604 " pdb=" C2' G 21604 " pdb=" N9 G 21604 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.14e-01 ... (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: 921.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 75.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1012.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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= 0.147 Angle : 0.548 7.843 38660 Z= 0.313 Chirality : 0.038 0.199 4714 Planarity : 0.004 0.046 3154 Dihedral : 20.587 179.691 13530 Min Nonbonded Distance : 1.309 Molprobity Statistics. All-atom Clashscore : 4.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP K 64 HIS 0.004 0.001 HIS R 29 PHE 0.016 0.002 PHE D 79 TYR 0.014 0.001 TYR F 188 ARG 0.004 0.000 ARG S 39 Details of bonding type rmsd hydrogen bonds : bond 0.12639 ( 1019) hydrogen bonds : angle 5.11115 ( 2469) metal coordination : bond 0.04713 ( 8) metal coordination : angle 2.61205 ( 12) covalent geometry : bond 0.00278 (26972) covalent geometry : angle 0.54616 (38648) *********************** 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 : 1.923 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: 1.5649 time to fit residues: 616.5987 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 : 2.112 ------------------------------------------------------------------------------- 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 200 optimal weight: 0.0980 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 83 ASN F 203 ASN P 103 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 = 0.3469 r_free = 0.3469 target = 0.129387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104014 restraints weight = 29131.567| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 0.96 r_work: 0.2931 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26980 Z= 0.111 Angle : 0.529 8.275 38660 Z= 0.278 Chirality : 0.037 0.203 4714 Planarity : 0.004 0.051 3154 Dihedral : 22.487 179.889 9602 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.51 % Allowed : 11.53 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1914 helix: 2.13 (0.20), residues: 664 sheet: 0.75 (0.26), residues: 377 loop : -0.51 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 132 HIS 0.003 0.001 HIS f 135 PHE 0.013 0.001 PHE K 67 TYR 0.013 0.001 TYR M 61 ARG 0.004 0.000 ARG T 121 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 1019) hydrogen bonds : angle 3.95541 ( 2469) metal coordination : bond 0.00337 ( 8) metal coordination : angle 3.42969 ( 12) covalent geometry : bond 0.00220 (26972) covalent geometry : angle 0.52546 (38648) *********************** 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 307 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 2.251 Fit side-chains REVERT: F 29 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6843 (pp30) REVERT: F 123 GLU cc_start: 0.8781 (tt0) cc_final: 0.8544 (tt0) REVERT: K 3 MET cc_start: 0.9308 (ptp) cc_final: 0.8602 (ptp) REVERT: K 82 TYR cc_start: 0.8636 (t80) cc_final: 0.8330 (t80) REVERT: K 90 VAL cc_start: 0.8061 (m) cc_final: 0.7845 (p) REVERT: P 37 TYR cc_start: 0.9117 (m-10) cc_final: 0.8895 (m-80) REVERT: S 115 LYS cc_start: 0.8402 (mttt) cc_final: 0.7954 (tmtt) REVERT: T 10 ASN cc_start: 0.8407 (t0) cc_final: 0.8194 (t0) REVERT: T 137 GLN cc_start: 0.8574 (mt0) cc_final: 0.8102 (mt0) REVERT: c 14 VAL cc_start: 0.9384 (t) cc_final: 0.9149 (t) REVERT: f 107 LYS cc_start: 0.6107 (pttp) cc_final: 0.5307 (tptm) REVERT: g 119 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7827 (mm-40) REVERT: g 165 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7649 (mt) REVERT: g 192 THR cc_start: 0.6965 (m) cc_final: 0.6603 (p) REVERT: g 230 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8240 (mt) outliers start: 42 outliers final: 20 residues processed: 293 average time/residue: 1.5829 time to fit residues: 529.5515 Evaluate side-chains 264 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 F residue 106 GLU Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 123 VAL 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 Z residue 49 LEU 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 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 64 optimal weight: 0.0980 chunk 148 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 220 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 103 ASN R 26 ASN U 81 GLN U 92 HIS ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102052 restraints weight = 29051.940| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 0.96 r_work: 0.2895 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26980 Z= 0.135 Angle : 0.536 8.991 38660 Z= 0.280 Chirality : 0.038 0.185 4714 Planarity : 0.004 0.054 3154 Dihedral : 22.391 179.242 9601 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.46 % Allowed : 12.60 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1914 helix: 2.17 (0.20), residues: 668 sheet: 0.84 (0.27), residues: 369 loop : -0.54 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 PHE 0.013 0.001 PHE K 67 TYR 0.013 0.001 TYR M 61 ARG 0.006 0.000 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 1019) hydrogen bonds : angle 3.80974 ( 2469) metal coordination : bond 0.00401 ( 8) metal coordination : angle 3.55235 ( 12) covalent geometry : bond 0.00274 (26972) covalent geometry : angle 0.53191 (38648) *********************** 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 309 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 1.993 Fit side-chains REVERT: F 29 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6933 (pp30) REVERT: F 38 TYR cc_start: 0.8903 (m-80) cc_final: 0.8495 (m-80) REVERT: K 3 MET cc_start: 0.9340 (ptp) cc_final: 0.8691 (ptp) REVERT: K 46 MET cc_start: 0.8306 (mtp) cc_final: 0.7770 (mtp) REVERT: K 82 TYR cc_start: 0.8647 (t80) cc_final: 0.8332 (t80) REVERT: K 90 VAL cc_start: 0.8100 (m) cc_final: 0.7849 (p) REVERT: P 37 TYR cc_start: 0.9131 (m-10) cc_final: 0.8862 (m-80) REVERT: R 19 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8317 (ttmt) REVERT: R 23 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8049 (mtt180) REVERT: S 76 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: S 115 LYS cc_start: 0.8451 (mttt) cc_final: 0.7982 (tmtt) REVERT: T 88 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8579 (mtt) REVERT: T 137 GLN cc_start: 0.8614 (mt0) cc_final: 0.8139 (mt0) REVERT: c 14 VAL cc_start: 0.9399 (t) cc_final: 0.9159 (t) REVERT: f 107 LYS cc_start: 0.6005 (pttp) cc_final: 0.5313 (tptm) REVERT: g 165 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7626 (mt) REVERT: g 192 THR cc_start: 0.7001 (m) cc_final: 0.6650 (p) REVERT: g 230 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8298 (mm) REVERT: g 270 LEU cc_start: 0.7642 (mt) cc_final: 0.7079 (mm) REVERT: g 311 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.4957 (tm130) outliers start: 58 outliers final: 32 residues processed: 284 average time/residue: 2.0183 time to fit residues: 655.8462 Evaluate side-chains 279 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU 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 75 SER Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain K residue 64 TRP 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 19 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain S residue 76 GLN 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 T residue 88 MET 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 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 56 GLN 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 230 LEU Chi-restraints excluded: chain g residue 265 ILE 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 171 optimal weight: 5.9990 chunk 236 optimal weight: 0.0970 chunk 113 optimal weight: 0.5980 chunk 163 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 8 GLN R 26 ASN T 10 ASN U 81 GLN U 92 HIS c 29 GLN g 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104214 restraints weight = 29337.882| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 0.92 r_work: 0.2930 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26980 Z= 0.105 Angle : 0.513 8.573 38660 Z= 0.268 Chirality : 0.037 0.205 4714 Planarity : 0.004 0.054 3154 Dihedral : 22.339 179.990 9601 Min Nonbonded Distance : 1.178 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.17 % Allowed : 13.74 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1914 helix: 2.33 (0.20), residues: 662 sheet: 0.86 (0.27), residues: 364 loop : -0.52 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 132 HIS 0.003 0.001 HIS T 42 PHE 0.012 0.001 PHE K 67 TYR 0.012 0.001 TYR M 61 ARG 0.007 0.000 ARG Q 27 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1019) hydrogen bonds : angle 3.70013 ( 2469) metal coordination : bond 0.00318 ( 8) metal coordination : angle 3.31826 ( 12) covalent geometry : bond 0.00209 (26972) covalent geometry : angle 0.50977 (38648) *********************** 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 301 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 1.992 Fit side-chains REVERT: F 29 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7035 (pp30) REVERT: K 3 MET cc_start: 0.9297 (ptp) cc_final: 0.8630 (ptp) REVERT: K 46 MET cc_start: 0.8253 (mtp) cc_final: 0.7743 (mtp) REVERT: K 82 TYR cc_start: 0.8645 (t80) cc_final: 0.8394 (t80) REVERT: K 90 VAL cc_start: 0.8164 (m) cc_final: 0.7876 (p) REVERT: P 37 TYR cc_start: 0.9085 (m-10) cc_final: 0.8853 (m-80) REVERT: R 19 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8400 (ttmt) REVERT: S 76 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: S 115 LYS cc_start: 0.8439 (mttt) cc_final: 0.8015 (tmtt) REVERT: T 88 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8546 (mtt) REVERT: T 137 GLN cc_start: 0.8587 (mt0) cc_final: 0.8121 (mt0) REVERT: U 99 LYS cc_start: 0.7031 (pttt) cc_final: 0.6807 (pttp) REVERT: c 14 VAL cc_start: 0.9395 (t) cc_final: 0.9159 (t) REVERT: f 107 LYS cc_start: 0.5930 (pttp) cc_final: 0.5201 (tptm) REVERT: g 5 MET cc_start: 0.8215 (mmm) cc_final: 0.7626 (mtt) REVERT: g 56 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: g 165 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7676 (mt) REVERT: g 192 THR cc_start: 0.7033 (m) cc_final: 0.6724 (p) REVERT: g 230 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8332 (mm) REVERT: g 270 LEU cc_start: 0.7673 (mt) cc_final: 0.7145 (mm) outliers start: 53 outliers final: 28 residues processed: 279 average time/residue: 1.5235 time to fit residues: 486.9836 Evaluate side-chains 273 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU 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 106 GLU Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 64 TRP 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 72 VAL Chi-restraints excluded: chain R residue 19 LYS 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 T residue 88 MET 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 c residue 23 SER 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 56 GLN 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 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 75 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN R 26 ASN U 81 GLN U 92 HIS c 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097184 restraints weight = 30171.180| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 0.90 r_work: 0.2886 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26980 Z= 0.204 Angle : 0.595 9.077 38660 Z= 0.309 Chirality : 0.041 0.200 4714 Planarity : 0.005 0.055 3154 Dihedral : 22.412 178.717 9601 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.18 % Allowed : 13.26 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1914 helix: 2.13 (0.20), residues: 668 sheet: 0.78 (0.27), residues: 373 loop : -0.64 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 132 HIS 0.006 0.001 HIS R 29 PHE 0.013 0.002 PHE Q 132 TYR 0.017 0.002 TYR D 107 ARG 0.004 0.001 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1019) hydrogen bonds : angle 3.85980 ( 2469) metal coordination : bond 0.00386 ( 8) metal coordination : angle 3.79438 ( 12) covalent geometry : bond 0.00425 (26972) covalent geometry : angle 0.59139 (38648) *********************** 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 312 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 242 time to evaluate : 2.284 Fit side-chains REVERT: F 29 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6889 (pp30) REVERT: F 38 TYR cc_start: 0.8981 (m-80) cc_final: 0.8560 (m-80) REVERT: F 122 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7315 (mtm180) REVERT: K 3 MET cc_start: 0.9285 (ptp) cc_final: 0.8572 (ptp) REVERT: K 82 TYR cc_start: 0.8633 (t80) cc_final: 0.8265 (t80) REVERT: K 90 VAL cc_start: 0.8128 (m) cc_final: 0.7699 (p) REVERT: P 37 TYR cc_start: 0.9191 (m-10) cc_final: 0.8935 (m-80) REVERT: R 19 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8334 (ttmt) REVERT: S 76 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: T 8 ASP cc_start: 0.8444 (m-30) cc_final: 0.8179 (m-30) REVERT: T 137 GLN cc_start: 0.8602 (mt0) cc_final: 0.8105 (mt0) REVERT: f 107 LYS cc_start: 0.6146 (pttp) cc_final: 0.5313 (tptt) REVERT: g 5 MET cc_start: 0.8249 (mmm) cc_final: 0.7798 (mtt) REVERT: g 165 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7651 (mt) REVERT: g 192 THR cc_start: 0.7117 (m) cc_final: 0.6723 (p) REVERT: g 225 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7413 (pmtt) REVERT: g 230 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8280 (mm) outliers start: 70 outliers final: 36 residues processed: 283 average time/residue: 1.8042 time to fit residues: 587.2873 Evaluate side-chains 281 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU 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 75 SER Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain K residue 21 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 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 19 LYS 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 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 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 76 ARG 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 23 THR Chi-restraints excluded: chain g residue 30 MET 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 225 LYS 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 80 optimal weight: 0.0020 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 142 optimal weight: 0.0020 chunk 1 optimal weight: 4.9990 chunk 152 optimal weight: 0.0070 chunk 189 optimal weight: 0.8980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 97 GLN Q 142 GLN R 26 ASN U 81 GLN U 92 HIS c 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100337 restraints weight = 29063.715| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.07 r_work: 0.2873 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26980 Z= 0.103 Angle : 0.541 8.685 38660 Z= 0.282 Chirality : 0.037 0.207 4714 Planarity : 0.004 0.054 3154 Dihedral : 22.458 179.463 9599 Min Nonbonded Distance : 1.153 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.99 % Allowed : 15.05 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1914 helix: 2.32 (0.20), residues: 661 sheet: 0.82 (0.27), residues: 367 loop : -0.57 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 132 HIS 0.002 0.001 HIS Z 103 PHE 0.013 0.001 PHE K 67 TYR 0.015 0.001 TYR f 140 ARG 0.007 0.000 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1019) hydrogen bonds : angle 3.76839 ( 2469) metal coordination : bond 0.00319 ( 8) metal coordination : angle 3.18930 ( 12) covalent geometry : bond 0.00198 (26972) covalent geometry : angle 0.53812 (38648) *********************** 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 295 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 3.291 Fit side-chains REVERT: F 29 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.6912 (pp30) REVERT: F 38 TYR cc_start: 0.8947 (m-80) cc_final: 0.8491 (m-80) REVERT: K 3 MET cc_start: 0.9266 (ptp) cc_final: 0.8586 (ptp) REVERT: K 82 TYR cc_start: 0.8591 (t80) cc_final: 0.8187 (t80) REVERT: K 90 VAL cc_start: 0.8070 (m) cc_final: 0.7678 (p) REVERT: P 37 TYR cc_start: 0.9167 (m-10) cc_final: 0.8910 (m-80) REVERT: S 8 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7586 (pttt) REVERT: S 76 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: S 115 LYS cc_start: 0.8497 (mttt) cc_final: 0.7874 (tmtm) REVERT: T 8 ASP cc_start: 0.8584 (m-30) cc_final: 0.8322 (m-30) REVERT: T 137 GLN cc_start: 0.8598 (mt0) cc_final: 0.8145 (mt0) REVERT: f 107 LYS cc_start: 0.6082 (pttp) cc_final: 0.5373 (tptt) REVERT: g 128 THR cc_start: 0.8880 (m) cc_final: 0.8593 (p) REVERT: g 165 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7654 (mt) REVERT: g 192 THR cc_start: 0.7108 (m) cc_final: 0.6742 (p) REVERT: g 225 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7506 (pmtt) REVERT: g 230 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8198 (mm) outliers start: 50 outliers final: 28 residues processed: 275 average time/residue: 2.1518 time to fit residues: 682.0172 Evaluate side-chains 271 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 106 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 72 VAL 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 Z residue 49 LEU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 23 THR 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 189 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 225 LYS Chi-restraints excluded: chain g residue 230 LEU 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 38 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 19 GLN P 114 HIS R 26 ASN U 81 GLN U 92 HIS c 29 GLN ** g 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.094403 restraints weight = 29468.233| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.09 r_work: 0.2773 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 26980 Z= 0.372 Angle : 0.754 9.858 38660 Z= 0.385 Chirality : 0.050 0.241 4714 Planarity : 0.006 0.068 3154 Dihedral : 22.580 178.721 9599 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.88 % Allowed : 14.81 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1914 helix: 1.79 (0.20), residues: 664 sheet: 0.58 (0.27), residues: 374 loop : -0.86 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 64 HIS 0.008 0.002 HIS T 42 PHE 0.020 0.003 PHE Q 132 TYR 0.024 0.003 TYR D 107 ARG 0.007 0.001 ARG T 102 Details of bonding type rmsd hydrogen bonds : bond 0.06601 ( 1019) hydrogen bonds : angle 4.09328 ( 2469) metal coordination : bond 0.00535 ( 8) metal coordination : angle 4.41620 ( 12) covalent geometry : bond 0.00784 (26972) covalent geometry : angle 0.74969 (38648) *********************** 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 303 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 2.107 Fit side-chains REVERT: F 29 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: F 122 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7322 (mtm180) REVERT: K 3 MET cc_start: 0.9264 (ptp) cc_final: 0.8621 (ptp) REVERT: K 60 GLU cc_start: 0.8961 (tt0) cc_final: 0.8702 (tt0) REVERT: K 82 TYR cc_start: 0.8754 (t80) cc_final: 0.8277 (t80) REVERT: M 76 LEU cc_start: 0.6759 (tp) cc_final: 0.6364 (mt) REVERT: P 46 ASN cc_start: 0.8890 (t0) cc_final: 0.8663 (t0) REVERT: S 76 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: T 8 ASP cc_start: 0.8621 (m-30) cc_final: 0.8399 (m-30) REVERT: c 14 VAL cc_start: 0.9431 (t) cc_final: 0.9214 (t) REVERT: f 107 LYS cc_start: 0.6084 (pttp) cc_final: 0.5342 (tptt) REVERT: g 5 MET cc_start: 0.8215 (mmm) cc_final: 0.7898 (mtt) REVERT: g 225 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7497 (pmtt) REVERT: g 230 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (mm) outliers start: 65 outliers final: 41 residues processed: 276 average time/residue: 1.4863 time to fit residues: 469.5958 Evaluate side-chains 276 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 75 SER 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 21 MET Chi-restraints excluded: chain K residue 54 SER 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 S residue 76 GLN 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 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 23 THR Chi-restraints excluded: chain g residue 30 MET 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 225 LYS Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 188 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3367 r_free = 0.3367 target = 0.121434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107118 restraints weight = 29271.958| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.45 r_work: 0.2854 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26980 Z= 0.252 Angle : 0.648 9.365 38660 Z= 0.337 Chirality : 0.044 0.216 4714 Planarity : 0.006 0.089 3154 Dihedral : 22.533 178.983 9599 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.17 % Allowed : 16.43 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1914 helix: 1.77 (0.20), residues: 666 sheet: 0.57 (0.27), residues: 370 loop : -0.91 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 64 HIS 0.006 0.001 HIS R 29 PHE 0.014 0.002 PHE Q 132 TYR 0.019 0.002 TYR D 107 ARG 0.005 0.001 ARG T 102 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 1019) hydrogen bonds : angle 3.97092 ( 2469) metal coordination : bond 0.00378 ( 8) metal coordination : angle 4.03948 ( 12) covalent geometry : bond 0.00528 (26972) covalent geometry : angle 0.64455 (38648) *********************** 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 294 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 2.063 Fit side-chains REVERT: F 29 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: K 1 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8362 (ttt) REVERT: K 60 GLU cc_start: 0.8858 (tt0) cc_final: 0.8612 (tt0) REVERT: K 82 TYR cc_start: 0.8735 (t80) cc_final: 0.8308 (t80) REVERT: M 76 LEU cc_start: 0.6752 (tp) cc_final: 0.6406 (mt) REVERT: R 19 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8429 (ttmt) REVERT: S 76 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: c 14 VAL cc_start: 0.9423 (t) cc_final: 0.9200 (t) REVERT: c 33 GLU cc_start: 0.7220 (pp20) cc_final: 0.7005 (pp20) REVERT: f 107 LYS cc_start: 0.6183 (pttp) cc_final: 0.5404 (tptt) REVERT: g 5 MET cc_start: 0.8330 (mmm) cc_final: 0.7933 (mtt) REVERT: g 225 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7633 (pmtt) REVERT: g 230 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8380 (mm) outliers start: 53 outliers final: 36 residues processed: 272 average time/residue: 1.4842 time to fit residues: 460.7873 Evaluate side-chains 278 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 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 Q residue 7 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 6 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 U residue 115 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 76 ARG 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 23 THR Chi-restraints excluded: chain g residue 30 MET 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 225 LYS Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 98 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 81 GLN U 92 HIS c 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.097014 restraints weight = 29232.383| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 0.82 r_work: 0.2827 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26980 Z= 0.239 Angle : 0.639 9.287 38660 Z= 0.332 Chirality : 0.044 0.209 4714 Planarity : 0.005 0.083 3154 Dihedral : 22.489 178.983 9599 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.46 % Allowed : 16.25 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1914 helix: 1.75 (0.20), residues: 667 sheet: 0.52 (0.27), residues: 370 loop : -0.93 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 64 HIS 0.005 0.001 HIS T 42 PHE 0.013 0.002 PHE Q 132 TYR 0.019 0.002 TYR D 107 ARG 0.005 0.001 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 1019) hydrogen bonds : angle 3.95520 ( 2469) metal coordination : bond 0.00354 ( 8) metal coordination : angle 4.02301 ( 12) covalent geometry : bond 0.00500 (26972) covalent geometry : angle 0.63527 (38648) *********************** 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 302 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 2.090 Fit side-chains REVERT: F 29 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: F 122 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7214 (mtm180) REVERT: K 1 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8279 (ttt) REVERT: K 60 GLU cc_start: 0.8870 (tt0) cc_final: 0.8653 (tt0) REVERT: K 82 TYR cc_start: 0.8723 (t80) cc_final: 0.8304 (t80) REVERT: M 76 LEU cc_start: 0.6688 (tp) cc_final: 0.6360 (mt) REVERT: R 19 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8429 (ttmt) REVERT: S 76 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: c 14 VAL cc_start: 0.9432 (t) cc_final: 0.9210 (t) REVERT: c 33 GLU cc_start: 0.7112 (pp20) cc_final: 0.6892 (pp20) REVERT: f 107 LYS cc_start: 0.6104 (pttp) cc_final: 0.5357 (tptt) REVERT: g 225 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7682 (pmtt) REVERT: g 230 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8377 (mm) outliers start: 58 outliers final: 40 residues processed: 278 average time/residue: 1.5266 time to fit residues: 484.5502 Evaluate side-chains 287 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 75 SER 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 K residue 21 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 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 R residue 6 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 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 69 THR Chi-restraints excluded: chain Z residue 76 ARG 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 23 THR 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 184 LEU Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 225 LYS Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 297 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 15 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 190 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 12 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 = 0.3421 r_free = 0.3421 target = 0.125628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096855 restraints weight = 29282.171| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.99 r_work: 0.2856 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26980 Z= 0.119 Angle : 0.546 9.891 38660 Z= 0.286 Chirality : 0.038 0.211 4714 Planarity : 0.004 0.077 3154 Dihedral : 22.358 178.401 9598 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 17.20 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1914 helix: 2.07 (0.20), residues: 661 sheet: 0.67 (0.28), residues: 356 loop : -0.81 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 PHE 0.027 0.001 PHE D 79 TYR 0.013 0.001 TYR D 107 ARG 0.006 0.000 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 1019) hydrogen bonds : angle 3.74249 ( 2469) metal coordination : bond 0.00295 ( 8) metal coordination : angle 3.51938 ( 12) covalent geometry : bond 0.00242 (26972) covalent geometry : angle 0.54253 (38648) ********************** 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: 41 poor density : 264 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: D 81 GLU cc_start: 0.6638 (mp0) cc_final: 0.6196 (mp0) REVERT: F 29 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7077 (pp30) REVERT: F 38 TYR cc_start: 0.8961 (m-80) cc_final: 0.8550 (m-80) REVERT: K 60 GLU cc_start: 0.8811 (tt0) cc_final: 0.8592 (tt0) REVERT: K 82 TYR cc_start: 0.8698 (t80) cc_final: 0.8317 (t80) REVERT: K 90 VAL cc_start: 0.8042 (m) cc_final: 0.7602 (p) REVERT: M 76 LEU cc_start: 0.6591 (tp) cc_final: 0.6230 (mt) REVERT: R 19 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8394 (ttmt) REVERT: S 76 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: S 115 LYS cc_start: 0.8533 (mttt) cc_final: 0.7993 (tmtm) REVERT: U 34 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8407 (tttt) REVERT: c 14 VAL cc_start: 0.9418 (t) cc_final: 0.9182 (t) REVERT: c 33 GLU cc_start: 0.7198 (pp20) cc_final: 0.6922 (pp20) REVERT: f 107 LYS cc_start: 0.6108 (pttp) cc_final: 0.5332 (tptt) REVERT: g 5 MET cc_start: 0.8320 (mmm) cc_final: 0.7812 (mtt) REVERT: g 192 THR cc_start: 0.7051 (m) cc_final: 0.6803 (p) REVERT: g 225 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7686 (pmtt) REVERT: g 230 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mm) outliers start: 41 outliers final: 28 residues processed: 288 average time/residue: 1.5309 time to fit residues: 506.7053 Evaluate side-chains 289 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 106 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 31 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 76 GLN 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 97 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 76 ARG 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 23 THR 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 225 LYS Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 45 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096085 restraints weight = 29987.926| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 0.94 r_work: 0.2863 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26980 Z= 0.200 Angle : 0.600 11.438 38660 Z= 0.312 Chirality : 0.041 0.203 4714 Planarity : 0.005 0.072 3154 Dihedral : 22.364 178.449 9598 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.45 % Allowed : 17.38 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1914 helix: 1.98 (0.20), residues: 661 sheet: 0.56 (0.27), residues: 368 loop : -0.79 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 64 HIS 0.005 0.001 HIS R 29 PHE 0.024 0.002 PHE D 79 TYR 0.014 0.002 TYR D 107 ARG 0.006 0.000 ARG P 50 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 1019) hydrogen bonds : angle 3.82475 ( 2469) metal coordination : bond 0.00338 ( 8) metal coordination : angle 3.83538 ( 12) covalent geometry : bond 0.00417 (26972) covalent geometry : angle 0.59591 (38648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21025.83 seconds wall clock time: 370 minutes 27.12 seconds (22227.12 seconds total)