Starting phenix.real_space_refine on Mon Aug 10 08:17:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.map" model { file = "/net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xai_66688/08_2026/9xai_66688.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 1 6.06 5 P 1141 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 23733 2.51 5 N 8282 2.21 5 O 11488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44705 Number of models: 1 Model: "" Number of chains: 22 Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1723 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "H" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2072 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain: "J" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1875 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 14, 'TRANS': 217} Chain: "K" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1562 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1621 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "M" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1466 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "O" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1222 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "Q" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1182 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "R" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1002 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "a" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1099 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "b" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1061 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "e" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 611 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 6, 'TRANS': 74} Chain: "h" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 181 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "A" Number of atoms: 24337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 24337 Classifications: {'RNA': 1141} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 77, 'rna3p_pur': 508, 'rna3p_pyr': 453} Link IDs: {'rna2p': 179, 'rna3p': 961} Chain breaks: 5 Chain: "1" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "3" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "6" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "8" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 537 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17217 SG CYS e 40 59.340 154.009 142.794 1.00 99.06 S Time building chain proxies: 7.57, per 1000 atoms: 0.17 Number of scatterers: 44705 At special positions: 0 Unit cell: (190.19, 230.945, 173.47, 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 1 29.99 S 58 16.00 P 1141 15.00 Mg 2 11.99 O 11488 8.00 N 8282 7.00 C 23733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN e 101 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 40 " 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4718 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 25 sheets defined 38.0% alpha, 18.6% beta 376 base pairs and 613 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.666A pdb=" N ARG E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'H' and resid 15 through 19 Processing helix chain 'H' and resid 44 through 49 Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 116 through 119 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 246 through 262 Processing helix chain 'J' and resid 20 through 28 removed outlier: 4.246A pdb=" N LEU J 24 " --> pdb=" O ASP J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 42 removed outlier: 3.661A pdb=" N GLY J 42 " --> pdb=" O ASP J 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 42' Processing helix chain 'J' and resid 137 through 146 Processing helix chain 'J' and resid 152 through 156 Processing helix chain 'J' and resid 183 through 231 removed outlier: 4.291A pdb=" N LYS J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.720A pdb=" N ASN K 7 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 37 Processing helix chain 'K' and resid 40 through 44 removed outlier: 3.926A pdb=" N LEU K 44 " --> pdb=" O LYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 79 removed outlier: 3.544A pdb=" N VAL K 79 " --> pdb=" O GLY K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 123 through 126 Processing helix chain 'K' and resid 127 through 140 removed outlier: 3.812A pdb=" N VAL K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 87 through 94 removed outlier: 3.651A pdb=" N VAL L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 117 Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 140 through 154 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 176 through 181 Processing helix chain 'L' and resid 190 through 201 removed outlier: 3.777A pdb=" N ALA L 194 " --> pdb=" O GLY L 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 37 through 59 Processing helix chain 'M' and resid 64 through 81 removed outlier: 3.697A pdb=" N ILE M 81 " --> pdb=" O ARG M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.665A pdb=" N PHE M 102 " --> pdb=" O LYS M 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 114 Processing helix chain 'M' and resid 119 through 129 removed outlier: 3.544A pdb=" N GLN M 129 " --> pdb=" O VAL M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 152 No H-bonds generated for 'chain 'M' and resid 150 through 152' Processing helix chain 'M' and resid 160 through 164 removed outlier: 3.700A pdb=" N GLY M 164 " --> pdb=" O PRO M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 180 Processing helix chain 'O' and resid 50 through 54 Processing helix chain 'Q' and resid 29 through 43 removed outlier: 3.630A pdb=" N VAL Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 63 through 68 Processing helix chain 'Q' and resid 70 through 78 Processing helix chain 'Q' and resid 85 through 105 Processing helix chain 'Q' and resid 108 through 133 Processing helix chain 'Q' and resid 145 through 149 removed outlier: 3.586A pdb=" N LEU Q 149 " --> pdb=" O ALA Q 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 88 Processing helix chain 'R' and resid 108 through 121 removed outlier: 3.684A pdb=" N GLN R 112 " --> pdb=" O GLY R 108 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 20 removed outlier: 3.537A pdb=" N ASP Z 9 " --> pdb=" O SER Z 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET Z 20 " --> pdb=" O ASN Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 44 removed outlier: 3.825A pdb=" N VAL Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS Z 44 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 94 removed outlier: 3.950A pdb=" N TRP Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU Z 94 " --> pdb=" O VAL Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 113 through 120 Processing helix chain 'a' and resid 11 through 23 removed outlier: 3.614A pdb=" N LEU a 15 " --> pdb=" O ALA a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 35 Processing helix chain 'a' and resid 90 through 95 removed outlier: 3.638A pdb=" N LEU a 93 " --> pdb=" O ASP a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 137 removed outlier: 3.646A pdb=" N LYS a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'b' and resid 54 through 56 No H-bonds generated for 'chain 'b' and resid 54 through 56' Processing helix chain 'b' and resid 81 through 89 Processing helix chain 'b' and resid 90 through 97 Processing helix chain 'b' and resid 107 through 121 removed outlier: 3.671A pdb=" N LEU b 121 " --> pdb=" O ARG b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 133 removed outlier: 3.756A pdb=" N LYS b 131 " --> pdb=" O LYS b 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS b 133 " --> pdb=" O ALA b 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 16 Processing helix chain 'h' and resid 32 through 45 Processing helix chain '1' and resid 249 through 263 removed outlier: 3.691A pdb=" N LYS 1 263 " --> pdb=" O GLN 1 259 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 100 removed outlier: 4.174A pdb=" N ALA 3 94 " --> pdb=" O HIS 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 108 removed outlier: 3.857A pdb=" N ASP 3 107 " --> pdb=" O PRO 3 103 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 149 removed outlier: 4.286A pdb=" N LEU 3 136 " --> pdb=" O SER 3 132 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN 3 137 " --> pdb=" O ASN 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 161 Processing helix chain '3' and resid 179 through 192 Processing helix chain '3' and resid 195 through 205 Processing helix chain '3' and resid 221 through 238 removed outlier: 3.514A pdb=" N GLY 3 238 " --> pdb=" O SER 3 234 " (cutoff:3.500A) Processing helix chain '3' and resid 240 through 259 Processing helix chain '6' and resid 480 through 501 removed outlier: 3.585A pdb=" N LYS 6 484 " --> pdb=" O ASP 6 480 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 6 501 " --> pdb=" O GLU 6 497 " (cutoff:3.500A) Processing helix chain '6' and resid 504 through 517 removed outlier: 3.836A pdb=" N LYS 6 508 " --> pdb=" O PRO 6 504 " (cutoff:3.500A) Processing helix chain '8' and resid 404 through 433 Processing helix chain '8' and resid 438 through 451 Processing sheet with id=AA1, first strand: chain 'E' and resid 42 through 49 removed outlier: 6.414A pdb=" N ILE E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS E 45 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR E 30 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU E 47 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP E 28 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR E 98 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN E 95 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL E 91 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 97 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS E 85 " --> pdb=" O HIS E 101 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU E 103 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS E 83 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 42 through 49 removed outlier: 6.414A pdb=" N ILE E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS E 45 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR E 30 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU E 47 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP E 28 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR E 98 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 13.854A pdb=" N ASN E 99 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 13.445A pdb=" N LYS E 219 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N HIS E 101 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 217 " --> pdb=" O HIS E 101 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E 105 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ARG E 213 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N HIS E 211 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE E 142 " --> pdb=" O HIS E 211 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 213 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE E 140 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL E 215 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 138 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU E 217 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG E 136 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.874A pdb=" N PHE H 138 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL H 129 " --> pdb=" O PHE H 138 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL H 140 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 161 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP H 171 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP H 163 " --> pdb=" O ILE H 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE H 169 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 217 through 221 removed outlier: 3.896A pdb=" N HIS H 197 " --> pdb=" O HIS H 209 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS H 211 " --> pdb=" O ILE H 195 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE H 195 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU H 180 " --> pdb=" O ILE H 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 12 through 17 removed outlier: 6.139A pdb=" N LYS J 2 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU J 111 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN J 4 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE J 113 " --> pdb=" O ASN J 4 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER J 6 " --> pdb=" O ILE J 113 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LYS J 115 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 106 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP J 57 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL J 108 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY J 55 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA J 110 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE J 49 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 72 through 77 Processing sheet with id=AA9, first strand: chain 'J' and resid 160 through 162 Processing sheet with id=AB1, first strand: chain 'K' and resid 51 through 56 removed outlier: 6.972A pdb=" N LYS K 62 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU K 97 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE K 64 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU K 99 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE K 66 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 190 through 194 removed outlier: 4.377A pdb=" N ASN K 190 " --> pdb=" O LYS K 158 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS K 148 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE Z 50 " --> pdb=" O THR K 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 37 through 38 Processing sheet with id=AB4, first strand: chain 'L' and resid 46 through 47 removed outlier: 3.568A pdb=" N LYS L 54 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 62 through 67 removed outlier: 7.569A pdb=" N ILE L 78 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP L 105 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL L 101 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N GLY L 185 " --> pdb=" O SER L 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN L 64 " --> pdb=" O GLY L 185 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE L 187 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA L 66 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 137 through 138 Processing sheet with id=AB7, first strand: chain 'O' and resid 75 through 82 removed outlier: 17.996A pdb=" N ILE O 75 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 15.313A pdb=" N LEU O 96 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N THR O 77 " --> pdb=" O GLU O 94 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU O 94 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE O 90 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE O 142 " --> pdb=" O ALA O 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL O 144 " --> pdb=" O HIS O 115 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL O 129 " --> pdb=" O LEU O 145 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL O 147 " --> pdb=" O MET O 127 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N MET O 127 " --> pdb=" O VAL O 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 53 through 55 removed outlier: 6.799A pdb=" N GLY R 28 " --> pdb=" O HIS R 93 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS R 95 " --> pdb=" O GLY R 28 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA R 30 " --> pdb=" O LYS R 95 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG R 97 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE R 32 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU R 129 " --> pdb=" O ILE R 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Z' and resid 73 through 74 removed outlier: 3.813A pdb=" N GLY Z 123 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 73 through 74 removed outlier: 5.161A pdb=" N ILE Z 125 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR Z 105 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 49 through 56 removed outlier: 6.944A pdb=" N ARG a 73 " --> pdb=" O LEU a 54 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE a 122 " --> pdb=" O THR a 84 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU a 103 " --> pdb=" O VAL a 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 9 through 18 removed outlier: 4.504A pdb=" N PHE b 15 " --> pdb=" O GLN b 25 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN b 25 " --> pdb=" O PHE b 15 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG b 17 " --> pdb=" O ARG b 23 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG b 23 " --> pdb=" O ARG b 17 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS b 71 " --> pdb=" O THR b 65 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR b 65 " --> pdb=" O LYS b 71 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR b 73 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU b 63 " --> pdb=" O THR b 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 43 through 47 Processing sheet with id=AC5, first strand: chain 'e' and resid 64 through 65 Processing sheet with id=AC6, first strand: chain '3' and resid 82 through 86 Processing sheet with id=AC7, first strand: chain '3' and resid 165 through 170 858 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 909 hydrogen bonds 1408 hydrogen bond angles 0 basepair planarities 376 basepair parallelities 613 stacking parallelities Total time for adding SS restraints: 15.48 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5044 1.32 - 1.44: 19198 1.44 - 1.57: 21314 1.57 - 1.69: 2281 1.69 - 1.81: 94 Bond restraints: 47931 Sorted by residual: bond pdb=" C2 G A 352 " pdb=" N3 G A 352 " ideal model delta sigma weight residual 1.323 1.270 0.053 8.00e-03 1.56e+04 4.36e+01 bond pdb=" N3 G A 352 " pdb=" C4 G A 352 " ideal model delta sigma weight residual 1.350 1.308 0.042 7.00e-03 2.04e+04 3.57e+01 bond pdb=" C2 U A 117 " pdb=" N3 U A 117 " ideal model delta sigma weight residual 1.373 1.337 0.036 7.00e-03 2.04e+04 2.59e+01 bond pdb=" C2 C A 311 " pdb=" O2 C A 311 " ideal model delta sigma weight residual 1.240 1.195 0.045 9.00e-03 1.23e+04 2.49e+01 bond pdb=" C2 G A 352 " pdb=" N2 G A 352 " ideal model delta sigma weight residual 1.341 1.291 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 47926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 68573 2.83 - 5.65: 1436 5.65 - 8.48: 133 8.48 - 11.31: 18 11.31 - 14.14: 6 Bond angle restraints: 70166 Sorted by residual: angle pdb=" N2 G A 352 " pdb=" C2 G A 352 " pdb=" N3 G A 352 " ideal model delta sigma weight residual 119.90 110.22 9.68 7.00e-01 2.04e+00 1.91e+02 angle pdb=" N1 C A 450 " pdb=" C2 C A 450 " pdb=" O2 C A 450 " ideal model delta sigma weight residual 118.90 126.86 -7.96 6.00e-01 2.78e+00 1.76e+02 angle pdb=" C1' C A 450 " pdb=" N1 C A 450 " pdb=" C2 C A 450 " ideal model delta sigma weight residual 118.80 132.53 -13.73 1.10e+00 8.26e-01 1.56e+02 angle pdb=" N9 G A 352 " pdb=" C4 G A 352 " pdb=" C5 G A 352 " ideal model delta sigma weight residual 105.40 110.37 -4.97 4.00e-01 6.25e+00 1.54e+02 angle pdb=" O6 G A 352 " pdb=" C6 G A 352 " pdb=" N1 G A 352 " ideal model delta sigma weight residual 119.90 112.74 7.16 6.00e-01 2.78e+00 1.43e+02 ... (remaining 70161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 27300 35.63 - 71.25: 2842 71.25 - 106.88: 303 106.88 - 142.50: 9 142.50 - 178.13: 10 Dihedral angle restraints: 30464 sinusoidal: 23154 harmonic: 7310 Sorted by residual: dihedral pdb=" C5' U A1795 " pdb=" C4' U A1795 " pdb=" C3' U A1795 " pdb=" O3' U A1795 " ideal model delta sinusoidal sigma weight residual 147.00 82.30 64.70 1 8.00e+00 1.56e-02 8.59e+01 dihedral pdb=" C4' U A1795 " pdb=" C3' U A1795 " pdb=" C2' U A1795 " pdb=" C1' U A1795 " ideal model delta sinusoidal sigma weight residual -35.00 28.94 -63.94 1 8.00e+00 1.56e-02 8.41e+01 dihedral pdb=" O4' U A 74 " pdb=" C1' U A 74 " pdb=" N1 U A 74 " pdb=" C2 U A 74 " ideal model delta sinusoidal sigma weight residual 200.00 41.16 158.84 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 30461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 7139 0.089 - 0.179: 1561 0.179 - 0.268: 42 0.268 - 0.358: 10 0.358 - 0.447: 2 Chirality restraints: 8754 Sorted by residual: chirality pdb=" P A A 502 " pdb=" OP1 A A 502 " pdb=" OP2 A A 502 " pdb=" O5' A A 502 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C1' U A 859 " pdb=" O4' U A 859 " pdb=" C2' U A 859 " pdb=" N1 U A 859 " both_signs ideal model delta sigma weight residual False 2.47 2.09 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C2' U A 222 " pdb=" C3' U A 222 " pdb=" O2' U A 222 " pdb=" C1' U A 222 " both_signs ideal model delta sigma weight residual False -2.60 -2.28 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 8751 not shown) Planarity restraints: 4686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG h 37 " -0.850 9.50e-02 1.11e+02 3.81e-01 8.82e+01 pdb=" NE ARG h 37 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG h 37 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG h 37 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG h 37 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 352 " 0.007 2.00e-02 2.50e+03 3.64e-02 3.97e+01 pdb=" N9 G A 352 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 352 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 352 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A 352 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A 352 " -0.022 2.00e-02 2.50e+03 pdb=" O6 G A 352 " 0.029 2.00e-02 2.50e+03 pdb=" N1 G A 352 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 352 " -0.103 2.00e-02 2.50e+03 pdb=" N2 G A 352 " 0.059 2.00e-02 2.50e+03 pdb=" N3 G A 352 " 0.017 2.00e-02 2.50e+03 pdb=" C4 G A 352 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 311 " 0.016 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" N1 C A 311 " -0.012 2.00e-02 2.50e+03 pdb=" C2 C A 311 " 0.092 2.00e-02 2.50e+03 pdb=" O2 C A 311 " -0.069 2.00e-02 2.50e+03 pdb=" N3 C A 311 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 311 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C A 311 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 311 " -0.015 2.00e-02 2.50e+03 pdb=" C6 C A 311 " -0.017 2.00e-02 2.50e+03 ... (remaining 4683 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 3658 2.71 - 3.26: 39877 3.26 - 3.81: 88196 3.81 - 4.35: 107261 4.35 - 4.90: 151041 Nonbonded interactions: 390033 Sorted by model distance: nonbonded pdb=" O6 G A 874 " pdb=" O4 U A 933 " model vdw 2.168 2.432 nonbonded pdb=" O TYR H 27 " pdb=" O2' U A 444 " model vdw 2.209 3.040 nonbonded pdb=" O HOH A1901 " pdb=" O HOH A1904 " model vdw 2.213 3.040 nonbonded pdb=" O LYS 3 243 " pdb=" ND2 ASN 3 247 " model vdw 2.217 3.120 nonbonded pdb=" O ILE Q 53 " pdb=" OG SER Q 57 " model vdw 2.228 3.040 ... (remaining 390028 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 50.380 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.005 0.208 47932 Z= 0.394 Angle : 1.012 14.136 70166 Z= 0.846 Chirality : 0.064 0.447 8754 Planarity : 0.009 0.381 4686 Dihedral : 22.329 178.130 25746 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 0.37 % Allowed : 0.69 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2509 helix: -0.78 (0.17), residues: 831 sheet: -1.11 (0.23), residues: 452 loop : -1.37 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 72 TYR 0.035 0.003 TYR E 205 PHE 0.045 0.002 PHE E 100 TRP 0.096 0.003 TRP M 41 HIS 0.008 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.39 (47931) covalent geometry : angle 1.01197 / 0.85 (70166) hydrogen bonds : bond 0.12209 / 8.18 ( 1762) hydrogen bonds : angle 5.92906 / 4.13 ( 3820) metal coordination : bond 0.20808 / 10.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 542 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8968 (m-40) cc_final: 0.8601 (m-40) REVERT: E 42 ASP cc_start: 0.7283 (t70) cc_final: 0.6159 (p0) REVERT: E 99 ASN cc_start: 0.8790 (t0) cc_final: 0.8585 (t0) REVERT: H 198 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7070 (mtp85) REVERT: H 200 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7016 (mtp-110) REVERT: J 63 MET cc_start: 0.7224 (ptm) cc_final: 0.6860 (ptm) REVERT: J 150 ASP cc_start: 0.7311 (p0) cc_final: 0.6860 (p0) REVERT: K 74 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7479 (tm-30) REVERT: K 77 HIS cc_start: 0.8320 (m-70) cc_final: 0.7907 (m-70) REVERT: K 145 ILE cc_start: 0.9009 (mp) cc_final: 0.8709 (mm) REVERT: L 161 GLU cc_start: 0.7252 (tp30) cc_final: 0.6854 (tp30) REVERT: O 82 SER cc_start: 0.8602 (t) cc_final: 0.8396 (t) REVERT: Q 52 VAL cc_start: 0.7939 (t) cc_final: 0.7626 (p) REVERT: Z 103 ILE cc_start: 0.8249 (mp) cc_final: 0.8025 (mp) REVERT: a 55 GLU cc_start: 0.7374 (pp20) cc_final: 0.7030 (pp20) REVERT: a 71 CYS cc_start: 0.7277 (m) cc_final: 0.6849 (m) REVERT: a 75 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7821 (tm-30) REVERT: a 97 ASP cc_start: 0.7543 (m-30) cc_final: 0.7276 (m-30) REVERT: b 41 ASP cc_start: 0.8190 (t70) cc_final: 0.7839 (t0) REVERT: e 36 LYS cc_start: 0.7317 (ttmm) cc_final: 0.7019 (ttmm) REVERT: e 72 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7981 (ttp-110) REVERT: 3 99 TRP cc_start: 0.7161 (t60) cc_final: 0.6556 (t60) REVERT: 3 151 ASP cc_start: 0.7833 (t0) cc_final: 0.7404 (p0) REVERT: 3 170 ASP cc_start: 0.7960 (m-30) cc_final: 0.7458 (m-30) REVERT: 8 423 ARG cc_start: 0.7307 (ttm170) cc_final: 0.6942 (ttp80) REVERT: 8 428 LEU cc_start: 0.8268 (mt) cc_final: 0.8066 (tp) REVERT: 8 437 LYS cc_start: 0.5764 (mmmt) cc_final: 0.5386 (mmmt) REVERT: 8 440 ARG cc_start: 0.7253 (mtt180) cc_final: 0.7034 (mtt180) outliers start: 8 outliers final: 2 residues processed: 547 average time/residue: 0.2597 time to fit residues: 233.2581 Evaluate side-chains 437 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 435 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 50.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 HIS E 209 ASN H 201 HIS ** L 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Z 15 ASN ** b 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 GLN 3 247 ASN 6 515 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086792 restraints weight = 122815.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085963 restraints weight = 129147.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086861 restraints weight = 90761.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086499 restraints weight = 66589.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086577 restraints weight = 70642.803| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 47932 Z= 0.142 Angle : 0.569 9.284 70166 Z= 0.329 Chirality : 0.040 0.362 8754 Planarity : 0.006 0.078 4686 Dihedral : 23.162 177.021 20427 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.19 % Allowed : 4.86 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2509 helix: -0.09 (0.17), residues: 859 sheet: -1.23 (0.23), residues: 478 loop : -1.27 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 37 TYR 0.022 0.002 TYR K 179 PHE 0.025 0.002 PHE E 223 TRP 0.036 0.002 TRP M 41 HIS 0.006 0.001 HIS R 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (47931) covalent geometry : angle 0.56942 / 0.33 (70166) hydrogen bonds : bond 0.08583 / 6.00 ( 1762) hydrogen bonds : angle 4.97746 / 3.47 ( 3820) metal coordination : bond 0.02700 / 1.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 503 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7038 (mt-10) REVERT: H 66 MET cc_start: 0.7700 (mmt) cc_final: 0.7438 (mmt) REVERT: H 87 MET cc_start: 0.8297 (tpp) cc_final: 0.7664 (mpp) REVERT: H 200 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6870 (mtp-110) REVERT: J 1 MET cc_start: 0.8304 (tmm) cc_final: 0.8026 (tmm) REVERT: J 63 MET cc_start: 0.7335 (ptm) cc_final: 0.7004 (ptm) REVERT: J 150 ASP cc_start: 0.7460 (p0) cc_final: 0.7174 (p0) REVERT: K 77 HIS cc_start: 0.8332 (m-70) cc_final: 0.7838 (m-70) REVERT: M 41 TRP cc_start: 0.7989 (m-90) cc_final: 0.7713 (m-90) REVERT: O 82 SER cc_start: 0.8843 (t) cc_final: 0.8614 (t) REVERT: R 38 ASP cc_start: 0.7460 (t0) cc_final: 0.7217 (t0) REVERT: a 55 GLU cc_start: 0.7321 (pp20) cc_final: 0.6883 (pp20) REVERT: a 71 CYS cc_start: 0.7185 (m) cc_final: 0.6793 (m) REVERT: a 75 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7464 (tm-30) REVERT: a 97 ASP cc_start: 0.7405 (m-30) cc_final: 0.7078 (m-30) REVERT: b 37 ASN cc_start: 0.8058 (p0) cc_final: 0.7710 (p0) REVERT: b 42 GLU cc_start: 0.7547 (pp20) cc_final: 0.7205 (pp20) REVERT: 3 99 TRP cc_start: 0.7137 (t60) cc_final: 0.6179 (t60) REVERT: 8 412 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6806 (mtt180) REVERT: 8 423 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7154 (ttp80) outliers start: 4 outliers final: 0 residues processed: 505 average time/residue: 0.2411 time to fit residues: 200.5390 Evaluate side-chains 413 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 24 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 chunk 329 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 208 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 324 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 32 GLN Z 15 ASN ** b 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 ASN 6 515 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.111720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084264 restraints weight = 122532.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.083321 restraints weight = 137482.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084370 restraints weight = 92508.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084172 restraints weight = 69457.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084262 restraints weight = 71385.124| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 47932 Z= 0.213 Angle : 0.643 9.254 70166 Z= 0.354 Chirality : 0.044 0.363 8754 Planarity : 0.006 0.077 4686 Dihedral : 23.056 176.047 20427 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2509 helix: 0.17 (0.17), residues: 859 sheet: -1.35 (0.22), residues: 479 loop : -1.27 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 160 TYR 0.024 0.002 TYR K 179 PHE 0.025 0.002 PHE e 47 TRP 0.027 0.002 TRP E 29 HIS 0.012 0.001 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (47931) covalent geometry : angle 0.64324 / 0.35 (70166) hydrogen bonds : bond 0.08924 / 6.34 ( 1762) hydrogen bonds : angle 4.89165 / 3.41 ( 3820) metal coordination : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 487 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 ASP cc_start: 0.7187 (t70) cc_final: 0.5850 (p0) REVERT: H 60 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7146 (mt-10) REVERT: H 66 MET cc_start: 0.7710 (mmt) cc_final: 0.7418 (mmt) REVERT: H 189 MET cc_start: 0.7671 (tpp) cc_final: 0.7352 (tpp) REVERT: H 200 ARG cc_start: 0.7237 (ttm110) cc_final: 0.6842 (mtp-110) REVERT: H 249 GLU cc_start: 0.8132 (pm20) cc_final: 0.7904 (pt0) REVERT: J 1 MET cc_start: 0.8428 (tmm) cc_final: 0.7169 (tmm) REVERT: J 63 MET cc_start: 0.7506 (ptm) cc_final: 0.7107 (ptm) REVERT: J 145 PHE cc_start: 0.7785 (m-80) cc_final: 0.7201 (m-10) REVERT: J 150 ASP cc_start: 0.7544 (p0) cc_final: 0.7182 (p0) REVERT: K 74 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7399 (tm-30) REVERT: K 145 ILE cc_start: 0.9038 (mp) cc_final: 0.8827 (mm) REVERT: M 59 THR cc_start: 0.8342 (p) cc_final: 0.8077 (t) REVERT: O 82 SER cc_start: 0.9134 (t) cc_final: 0.8884 (t) REVERT: Q 52 VAL cc_start: 0.8012 (t) cc_final: 0.7698 (p) REVERT: Z 103 ILE cc_start: 0.8199 (mp) cc_final: 0.7982 (mp) REVERT: a 55 GLU cc_start: 0.7444 (pp20) cc_final: 0.6917 (pp20) REVERT: a 71 CYS cc_start: 0.7213 (m) cc_final: 0.6929 (m) REVERT: a 75 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7554 (tm-30) REVERT: a 94 ASN cc_start: 0.8369 (p0) cc_final: 0.7835 (t0) REVERT: b 37 ASN cc_start: 0.8073 (p0) cc_final: 0.7816 (p0) REVERT: b 41 ASP cc_start: 0.7777 (t0) cc_final: 0.7109 (t0) REVERT: e 36 LYS cc_start: 0.7239 (ttmm) cc_final: 0.6935 (ttmm) REVERT: 3 99 TRP cc_start: 0.7122 (t60) cc_final: 0.6227 (t60) REVERT: 8 412 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6694 (mtt180) outliers start: 3 outliers final: 1 residues processed: 489 average time/residue: 0.2446 time to fit residues: 196.8491 Evaluate side-chains 400 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 247 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 342 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 283 optimal weight: 50.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 HIS J 129 HIS Q 32 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 HIS ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081300 restraints weight = 123567.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080849 restraints weight = 140160.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081325 restraints weight = 91822.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080922 restraints weight = 69852.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.081109 restraints weight = 74868.715| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 47932 Z= 0.352 Angle : 0.842 12.519 70166 Z= 0.438 Chirality : 0.055 0.410 8754 Planarity : 0.007 0.089 4686 Dihedral : 23.183 174.503 20427 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.14 % Allowed : 6.11 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2509 helix: -0.07 (0.17), residues: 861 sheet: -1.53 (0.23), residues: 460 loop : -1.60 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG 1 269 TYR 0.032 0.003 TYR H 58 PHE 0.026 0.003 PHE 3 142 TRP 0.056 0.003 TRP E 29 HIS 0.014 0.002 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.35 (47931) covalent geometry : angle 0.84235 / 0.44 (70166) hydrogen bonds : bond 0.10482 / 7.49 ( 1762) hydrogen bonds : angle 5.18738 / 3.62 ( 3820) metal coordination : bond 0.00514 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 448 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8853 (m-40) cc_final: 0.8570 (m-40) REVERT: E 42 ASP cc_start: 0.7221 (t70) cc_final: 0.5914 (p0) REVERT: H 60 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7150 (mt-10) REVERT: H 189 MET cc_start: 0.7784 (tpp) cc_final: 0.6873 (ttt) REVERT: H 200 ARG cc_start: 0.7279 (ttm110) cc_final: 0.6929 (mtp-110) REVERT: J 1 MET cc_start: 0.8696 (tmm) cc_final: 0.7501 (tmm) REVERT: J 145 PHE cc_start: 0.7907 (m-80) cc_final: 0.7302 (m-10) REVERT: J 150 ASP cc_start: 0.7509 (p0) cc_final: 0.7177 (p0) REVERT: K 145 ILE cc_start: 0.8995 (mp) cc_final: 0.8720 (mm) REVERT: M 41 TRP cc_start: 0.8291 (m-10) cc_final: 0.7554 (m-90) REVERT: O 82 SER cc_start: 0.9218 (t) cc_final: 0.9014 (t) REVERT: Q 52 VAL cc_start: 0.8001 (t) cc_final: 0.7693 (p) REVERT: R 95 LYS cc_start: 0.8602 (tptp) cc_final: 0.8326 (tptt) REVERT: a 55 GLU cc_start: 0.7661 (pp20) cc_final: 0.7205 (pp20) REVERT: a 75 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7486 (tm-30) REVERT: b 37 ASN cc_start: 0.8328 (p0) cc_final: 0.8086 (p0) REVERT: b 41 ASP cc_start: 0.8017 (t0) cc_final: 0.7050 (t0) REVERT: b 42 GLU cc_start: 0.8087 (pp20) cc_final: 0.7558 (pp20) REVERT: b 110 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6726 (tm-30) REVERT: 3 99 TRP cc_start: 0.7324 (t60) cc_final: 0.6409 (t60) REVERT: 3 202 GLU cc_start: 0.7106 (tp30) cc_final: 0.6842 (mm-30) REVERT: 8 412 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6676 (mtt180) outliers start: 3 outliers final: 0 residues processed: 451 average time/residue: 0.2310 time to fit residues: 172.9650 Evaluate side-chains 374 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 267 optimal weight: 50.0000 chunk 125 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 243 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 334 optimal weight: 9.9990 chunk 304 optimal weight: 40.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 211 HIS H 224 ASN J 189 HIS L 179 GLN Q 32 GLN ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083714 restraints weight = 123399.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083460 restraints weight = 120760.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082743 restraints weight = 84464.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.082379 restraints weight = 73463.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082566 restraints weight = 71267.909| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 47932 Z= 0.264 Angle : 0.712 10.511 70166 Z= 0.384 Chirality : 0.048 0.381 8754 Planarity : 0.006 0.075 4686 Dihedral : 23.207 174.688 20427 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2509 helix: 0.15 (0.17), residues: 862 sheet: -1.57 (0.23), residues: 458 loop : -1.57 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 11 TYR 0.028 0.003 TYR a 38 PHE 0.027 0.002 PHE E 24 TRP 0.056 0.002 TRP E 29 HIS 0.013 0.002 HIS Z 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.26 (47931) covalent geometry : angle 0.71197 / 0.38 (70166) hydrogen bonds : bond 0.09481 / 6.79 ( 1762) hydrogen bonds : angle 5.05179 / 3.54 ( 3820) metal coordination : bond 0.00313 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 454 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8885 (m-40) cc_final: 0.8578 (m-40) REVERT: E 42 ASP cc_start: 0.7072 (t70) cc_final: 0.6028 (p0) REVERT: H 60 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7055 (mt-10) REVERT: J 1 MET cc_start: 0.8683 (tmm) cc_final: 0.7582 (tmm) REVERT: J 150 ASP cc_start: 0.7526 (p0) cc_final: 0.7189 (p0) REVERT: K 145 ILE cc_start: 0.8994 (mp) cc_final: 0.8777 (mm) REVERT: M 59 THR cc_start: 0.8267 (p) cc_final: 0.8056 (t) REVERT: M 104 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7834 (mm-30) REVERT: Q 52 VAL cc_start: 0.8038 (t) cc_final: 0.7715 (p) REVERT: R 142 LYS cc_start: 0.6669 (mtmm) cc_final: 0.6403 (mtmm) REVERT: Z 26 MET cc_start: 0.8263 (tmm) cc_final: 0.7982 (tmm) REVERT: a 55 GLU cc_start: 0.7224 (pp20) cc_final: 0.6906 (pp20) REVERT: a 75 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7489 (tm-30) REVERT: b 41 ASP cc_start: 0.8170 (t0) cc_final: 0.7075 (t0) REVERT: b 42 GLU cc_start: 0.7974 (pp20) cc_final: 0.7724 (pp20) REVERT: b 110 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6768 (tm-30) REVERT: e 36 LYS cc_start: 0.7457 (ttmm) cc_final: 0.7162 (tttm) REVERT: 3 99 TRP cc_start: 0.7212 (t60) cc_final: 0.6313 (t60) outliers start: 3 outliers final: 0 residues processed: 456 average time/residue: 0.2452 time to fit residues: 184.9866 Evaluate side-chains 378 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 273 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 329 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 224 ASN K 12 ASN K 74 GLN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 247 ASN 8 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.107733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079628 restraints weight = 124404.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077743 restraints weight = 119201.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078145 restraints weight = 108285.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078351 restraints weight = 87203.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078429 restraints weight = 82169.349| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 47932 Z= 0.412 Angle : 0.941 13.870 70166 Z= 0.480 Chirality : 0.061 0.465 8754 Planarity : 0.008 0.082 4686 Dihedral : 23.309 174.055 20427 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.37 % Favored : 91.59 % Rotamer: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2509 helix: -0.27 (0.16), residues: 866 sheet: -1.84 (0.22), residues: 460 loop : -1.83 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 20 TYR 0.028 0.003 TYR a 38 PHE 0.043 0.003 PHE O 120 TRP 0.039 0.003 TRP E 29 HIS 0.015 0.002 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.41 (47931) covalent geometry : angle 0.94088 / 0.48 (70166) hydrogen bonds : bond 0.11347 / 8.09 ( 1762) hydrogen bonds : angle 5.40936 / 3.79 ( 3820) metal coordination : bond 0.00452 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.9150 (m-40) cc_final: 0.8638 (m-40) REVERT: E 42 ASP cc_start: 0.7302 (t70) cc_final: 0.6268 (p0) REVERT: H 60 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7180 (mt-10) REVERT: H 189 MET cc_start: 0.7765 (tpp) cc_final: 0.7514 (mmm) REVERT: J 28 TYR cc_start: 0.8694 (m-80) cc_final: 0.7729 (m-80) REVERT: J 150 ASP cc_start: 0.7879 (p0) cc_final: 0.7539 (p0) REVERT: K 80 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8563 (tp-100) REVERT: K 145 ILE cc_start: 0.9007 (mp) cc_final: 0.8785 (mm) REVERT: L 94 ASN cc_start: 0.7969 (m-40) cc_final: 0.7479 (m-40) REVERT: Q 52 VAL cc_start: 0.8083 (t) cc_final: 0.7746 (p) REVERT: R 38 ASP cc_start: 0.6845 (t0) cc_final: 0.6642 (t0) REVERT: R 95 LYS cc_start: 0.8703 (tptp) cc_final: 0.8436 (tptt) REVERT: R 123 MET cc_start: 0.6992 (tpt) cc_final: 0.6748 (tpt) REVERT: Z 26 MET cc_start: 0.8308 (tmm) cc_final: 0.7960 (tmm) REVERT: Z 103 ILE cc_start: 0.8270 (mp) cc_final: 0.8046 (mp) REVERT: a 75 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7393 (tm-30) REVERT: b 37 ASN cc_start: 0.8330 (p0) cc_final: 0.8061 (p0) REVERT: b 42 GLU cc_start: 0.8362 (pp20) cc_final: 0.8151 (pp20) REVERT: b 110 GLN cc_start: 0.7076 (tm-30) cc_final: 0.6782 (tm-30) REVERT: e 7 LEU cc_start: 0.8567 (mp) cc_final: 0.8353 (mp) REVERT: h 41 THR cc_start: 0.8957 (m) cc_final: 0.8707 (p) REVERT: 6 489 MET cc_start: 0.6531 (ppp) cc_final: 0.6064 (tmm) outliers start: 1 outliers final: 1 residues processed: 428 average time/residue: 0.2596 time to fit residues: 180.5330 Evaluate side-chains 366 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 273 optimal weight: 50.0000 chunk 211 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 225 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 79 HIS E 173 GLN H 67 GLN L 88 ASN Z 15 ASN ** b 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 247 ASN 8 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.110864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084740 restraints weight = 123431.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083557 restraints weight = 141699.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082387 restraints weight = 93122.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082050 restraints weight = 75040.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082159 restraints weight = 71724.708| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 47932 Z= 0.167 Angle : 0.624 10.604 70166 Z= 0.351 Chirality : 0.042 0.349 8754 Planarity : 0.006 0.079 4686 Dihedral : 23.258 175.133 20427 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2509 helix: 0.02 (0.17), residues: 870 sheet: -1.51 (0.23), residues: 450 loop : -1.62 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 49 TYR 0.029 0.002 TYR K 183 PHE 0.021 0.002 PHE 3 142 TRP 0.032 0.002 TRP a 136 HIS 0.011 0.001 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (47931) covalent geometry : angle 0.62424 / 0.35 (70166) hydrogen bonds : bond 0.08739 / 6.25 ( 1762) hydrogen bonds : angle 4.97717 / 3.49 ( 3820) metal coordination : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 468 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8991 (m-40) cc_final: 0.8545 (m-40) REVERT: E 42 ASP cc_start: 0.7093 (t70) cc_final: 0.6266 (p0) REVERT: E 142 PHE cc_start: 0.7066 (m-10) cc_final: 0.6723 (m-10) REVERT: H 60 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6894 (mt-10) REVERT: H 66 MET cc_start: 0.7668 (mmt) cc_final: 0.7313 (mmt) REVERT: J 27 PHE cc_start: 0.7835 (m-10) cc_final: 0.7572 (m-80) REVERT: J 28 TYR cc_start: 0.8585 (m-80) cc_final: 0.7700 (m-80) REVERT: J 63 MET cc_start: 0.8075 (ptm) cc_final: 0.7701 (ptm) REVERT: J 150 ASP cc_start: 0.7850 (p0) cc_final: 0.7524 (p0) REVERT: K 80 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8547 (tp-100) REVERT: K 145 ILE cc_start: 0.8962 (mp) cc_final: 0.8654 (mm) REVERT: L 161 GLU cc_start: 0.7082 (tp30) cc_final: 0.6882 (tp30) REVERT: L 193 LEU cc_start: 0.7415 (mt) cc_final: 0.7191 (mt) REVERT: R 38 ASP cc_start: 0.7058 (t0) cc_final: 0.6667 (t0) REVERT: R 40 PHE cc_start: 0.6939 (m-10) cc_final: 0.6628 (m-10) REVERT: R 95 LYS cc_start: 0.8578 (tptp) cc_final: 0.8378 (tptt) REVERT: Z 69 LEU cc_start: 0.6421 (pt) cc_final: 0.6135 (tt) REVERT: Z 94 LEU cc_start: 0.8225 (mt) cc_final: 0.7972 (mp) REVERT: a 69 ARG cc_start: 0.7054 (mmp80) cc_final: 0.6147 (mmt-90) REVERT: a 75 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7458 (tm-30) REVERT: b 29 ASP cc_start: 0.8511 (p0) cc_final: 0.8032 (p0) REVERT: b 37 ASN cc_start: 0.8151 (p0) cc_final: 0.7861 (p0) REVERT: e 7 LEU cc_start: 0.8481 (mp) cc_final: 0.8242 (mp) REVERT: e 36 LYS cc_start: 0.7510 (ttmm) cc_final: 0.6846 (tttm) REVERT: 6 489 MET cc_start: 0.6717 (ppp) cc_final: 0.6404 (tmm) REVERT: 8 412 ARG cc_start: 0.7349 (mtt180) cc_final: 0.7079 (mtt180) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2565 time to fit residues: 196.5955 Evaluate side-chains 390 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 288 optimal weight: 20.0000 chunk 281 optimal weight: 50.0000 chunk 131 optimal weight: 0.3980 chunk 314 optimal weight: 40.0000 chunk 176 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 271 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 67 GLN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082758 restraints weight = 124330.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081670 restraints weight = 141033.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.082413 restraints weight = 99288.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082598 restraints weight = 79146.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082650 restraints weight = 77639.290| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47932 Z= 0.205 Angle : 0.657 10.381 70166 Z= 0.360 Chirality : 0.045 0.361 8754 Planarity : 0.006 0.075 4686 Dihedral : 23.159 175.116 20427 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2509 helix: 0.10 (0.17), residues: 866 sheet: -1.50 (0.23), residues: 454 loop : -1.56 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 92 TYR 0.027 0.002 TYR K 179 PHE 0.035 0.002 PHE Q 113 TRP 0.057 0.002 TRP E 29 HIS 0.014 0.001 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (47931) covalent geometry : angle 0.65704 / 0.36 (70166) hydrogen bonds : bond 0.08818 / 6.29 ( 1762) hydrogen bonds : angle 4.97480 / 3.49 ( 3820) metal coordination : bond 0.00148 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8818 (m-40) cc_final: 0.8431 (m-40) REVERT: E 42 ASP cc_start: 0.7002 (t70) cc_final: 0.6172 (p0) REVERT: H 60 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7050 (mt-10) REVERT: H 66 MET cc_start: 0.7675 (mmt) cc_final: 0.7273 (mmt) REVERT: J 27 PHE cc_start: 0.7727 (m-10) cc_final: 0.7476 (m-80) REVERT: J 63 MET cc_start: 0.8026 (ptm) cc_final: 0.7648 (ptm) REVERT: J 150 ASP cc_start: 0.7713 (p0) cc_final: 0.7380 (p0) REVERT: K 80 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8474 (tp-100) REVERT: L 94 ASN cc_start: 0.7863 (m-40) cc_final: 0.7441 (m-40) REVERT: L 198 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: M 98 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7948 (ptpp) REVERT: O 82 SER cc_start: 0.9180 (t) cc_final: 0.8963 (t) REVERT: Q 52 VAL cc_start: 0.7848 (t) cc_final: 0.7493 (p) REVERT: R 38 ASP cc_start: 0.7049 (t0) cc_final: 0.6713 (t0) REVERT: R 40 PHE cc_start: 0.6946 (m-10) cc_final: 0.6653 (m-10) REVERT: R 95 LYS cc_start: 0.8609 (tptp) cc_final: 0.8356 (tptt) REVERT: Z 69 LEU cc_start: 0.6480 (pt) cc_final: 0.6085 (tt) REVERT: Z 94 LEU cc_start: 0.8239 (mt) cc_final: 0.7935 (mp) REVERT: a 69 ARG cc_start: 0.7018 (mmp80) cc_final: 0.6191 (mmt-90) REVERT: a 75 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7522 (tm-30) REVERT: b 37 ASN cc_start: 0.8186 (p0) cc_final: 0.7915 (p0) REVERT: b 41 ASP cc_start: 0.8126 (t0) cc_final: 0.7907 (t0) REVERT: e 7 LEU cc_start: 0.8572 (mp) cc_final: 0.8300 (mp) REVERT: e 36 LYS cc_start: 0.7417 (ttmm) cc_final: 0.7108 (tttm) REVERT: 6 489 MET cc_start: 0.6716 (ppp) cc_final: 0.6420 (tmm) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2569 time to fit residues: 191.2245 Evaluate side-chains 390 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 72 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 355 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 330 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 224 ASN J 189 HIS ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 137 GLN 3 247 ASN 8 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083451 restraints weight = 123591.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082611 restraints weight = 128180.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082874 restraints weight = 92556.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082518 restraints weight = 70869.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082560 restraints weight = 71099.374| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 47932 Z= 0.279 Angle : 0.749 10.685 70166 Z= 0.399 Chirality : 0.050 0.392 8754 Planarity : 0.007 0.078 4686 Dihedral : 23.184 174.810 20427 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2509 helix: -0.08 (0.17), residues: 869 sheet: -1.65 (0.23), residues: 454 loop : -1.63 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 25 TYR 0.033 0.003 TYR E 155 PHE 0.025 0.003 PHE O 20 TRP 0.041 0.002 TRP E 29 HIS 0.013 0.002 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.28 (47931) covalent geometry : angle 0.74885 / 0.40 (70166) hydrogen bonds : bond 0.09521 / 6.80 ( 1762) hydrogen bonds : angle 5.10601 / 3.58 ( 3820) metal coordination : bond 0.00215 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8758 (m-40) cc_final: 0.8514 (m-40) REVERT: E 66 PHE cc_start: 0.7979 (m-80) cc_final: 0.7774 (m-80) REVERT: H 60 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7107 (mt-10) REVERT: H 66 MET cc_start: 0.7672 (mmt) cc_final: 0.7309 (mmt) REVERT: H 67 GLN cc_start: 0.7363 (tp40) cc_final: 0.7161 (tp-100) REVERT: J 27 PHE cc_start: 0.7725 (m-10) cc_final: 0.7508 (m-80) REVERT: J 150 ASP cc_start: 0.7717 (p0) cc_final: 0.7388 (p0) REVERT: K 80 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8358 (tp-100) REVERT: L 94 ASN cc_start: 0.7866 (m-40) cc_final: 0.7396 (m-40) REVERT: O 82 SER cc_start: 0.9210 (t) cc_final: 0.8997 (t) REVERT: Q 52 VAL cc_start: 0.7983 (t) cc_final: 0.7609 (p) REVERT: R 95 LYS cc_start: 0.8637 (tptp) cc_final: 0.8355 (tptt) REVERT: Z 9 ASP cc_start: 0.8081 (m-30) cc_final: 0.7739 (m-30) REVERT: a 69 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6150 (mmt-90) REVERT: a 75 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7484 (tm-30) REVERT: b 37 ASN cc_start: 0.8214 (p0) cc_final: 0.7930 (p0) REVERT: b 41 ASP cc_start: 0.7885 (t0) cc_final: 0.7163 (t0) REVERT: b 107 SER cc_start: 0.8994 (t) cc_final: 0.8790 (t) REVERT: b 110 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6832 (tm-30) REVERT: e 7 LEU cc_start: 0.8564 (mp) cc_final: 0.8255 (mp) REVERT: 3 138 MET cc_start: 0.6445 (tmm) cc_final: 0.6133 (tmm) REVERT: 6 489 MET cc_start: 0.6686 (ppp) cc_final: 0.6326 (tmm) REVERT: 8 412 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6809 (mtt180) REVERT: 8 427 ARG cc_start: 0.8022 (tmt170) cc_final: 0.7367 (tpt90) REVERT: 8 431 ILE cc_start: 0.7603 (pt) cc_final: 0.7350 (pt) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2541 time to fit residues: 180.4543 Evaluate side-chains 375 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 235 optimal weight: 50.0000 chunk 299 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082848 restraints weight = 124794.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081989 restraints weight = 144271.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082713 restraints weight = 99204.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082360 restraints weight = 74962.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082514 restraints weight = 70846.373| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 47932 Z= 0.299 Angle : 0.776 10.752 70166 Z= 0.411 Chirality : 0.051 0.406 8754 Planarity : 0.007 0.074 4686 Dihedral : 23.217 173.812 20427 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2509 helix: -0.14 (0.17), residues: 862 sheet: -1.68 (0.23), residues: 451 loop : -1.65 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 92 TYR 0.036 0.003 TYR J 28 PHE 0.025 0.003 PHE 3 146 TRP 0.034 0.002 TRP a 136 HIS 0.012 0.002 HIS Z 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.30 (47931) covalent geometry : angle 0.77631 / 0.41 (70166) hydrogen bonds : bond 0.09724 / 6.94 ( 1762) hydrogen bonds : angle 5.19619 / 3.64 ( 3820) metal coordination : bond 0.00260 / 0.14 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ASN cc_start: 0.8736 (m-40) cc_final: 0.8463 (m-40) REVERT: E 66 PHE cc_start: 0.8038 (m-80) cc_final: 0.7820 (m-80) REVERT: E 205 TYR cc_start: 0.8614 (t80) cc_final: 0.8233 (t80) REVERT: H 60 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7058 (mt-10) REVERT: H 66 MET cc_start: 0.7649 (mmt) cc_final: 0.7287 (mmt) REVERT: H 67 GLN cc_start: 0.7447 (tp40) cc_final: 0.7240 (tp-100) REVERT: J 27 PHE cc_start: 0.7813 (m-10) cc_final: 0.7604 (m-80) REVERT: J 150 ASP cc_start: 0.7781 (p0) cc_final: 0.7470 (p0) REVERT: K 80 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8307 (tp-100) REVERT: L 94 ASN cc_start: 0.7923 (m-40) cc_final: 0.7490 (m-40) REVERT: L 161 GLU cc_start: 0.7075 (tp30) cc_final: 0.6572 (tp30) REVERT: L 198 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8197 (ttp-110) REVERT: M 151 GLN cc_start: 0.7909 (pp30) cc_final: 0.7684 (pp30) REVERT: Q 52 VAL cc_start: 0.7973 (t) cc_final: 0.7605 (p) REVERT: a 69 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6231 (mmt-90) REVERT: a 75 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7472 (tm-30) REVERT: b 37 ASN cc_start: 0.8193 (p0) cc_final: 0.7851 (p0) REVERT: b 41 ASP cc_start: 0.8237 (t0) cc_final: 0.7999 (t0) REVERT: b 42 GLU cc_start: 0.8013 (pp20) cc_final: 0.7570 (pp20) REVERT: b 45 GLU cc_start: 0.7809 (mp0) cc_final: 0.7545 (mp0) REVERT: b 110 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6825 (tm-30) REVERT: e 7 LEU cc_start: 0.8594 (mp) cc_final: 0.8249 (mp) REVERT: 3 138 MET cc_start: 0.6473 (tmm) cc_final: 0.6200 (tmm) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.2516 time to fit residues: 179.5807 Evaluate side-chains 372 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 105 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 235 optimal weight: 50.0000 chunk 117 optimal weight: 0.1980 chunk 224 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 15 ASN ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 247 ASN 8 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084484 restraints weight = 123881.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.083568 restraints weight = 147668.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084596 restraints weight = 97800.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084429 restraints weight = 70758.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084496 restraints weight = 74434.541| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47932 Z= 0.143 Angle : 0.604 10.156 70166 Z= 0.339 Chirality : 0.040 0.350 8754 Planarity : 0.006 0.079 4686 Dihedral : 23.173 174.847 20427 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.16), residues: 2509 helix: 0.15 (0.17), residues: 868 sheet: -1.45 (0.23), residues: 452 loop : -1.47 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 92 TYR 0.043 0.002 TYR J 28 PHE 0.027 0.002 PHE O 20 TRP 0.064 0.003 TRP E 29 HIS 0.009 0.001 HIS K 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (47931) covalent geometry : angle 0.60371 / 0.34 (70166) hydrogen bonds : bond 0.08143 / 5.81 ( 1762) hydrogen bonds : angle 4.91113 / 3.44 ( 3820) metal coordination : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6248.60 seconds wall clock time: 109 minutes 41.21 seconds (6581.21 seconds total)