Starting phenix.real_space_refine on Fri Sep 11 05:38:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2026/6iac_4435.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 5208 2.51 5 N 1384 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8210 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2353 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1763 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1164 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 135} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1259 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "F" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1019 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 112 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 1.87, per 1000 atoms: 0.23 Number of scatterers: 8210 At special positions: 0 Unit cell: (126.497, 184.962, 255.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1595 8.00 N 1384 7.00 C 5208 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: 0.39 Conformation dependent library (CDL) restraints added in 391.5 milliseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 61.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.322A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.960A pdb=" N ILE A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 227 through 247 removed outlier: 4.174A pdb=" N THR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.522A pdb=" N GLY A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.567A pdb=" N THR A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.653A pdb=" N PHE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.721A pdb=" N ASP A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.583A pdb=" N LYS B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.585A pdb=" N LYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.651A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.562A pdb=" N ILE B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.567A pdb=" N LYS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.109A pdb=" N GLU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.626A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 14 through 19' Processing helix chain 'D' and resid 20 through 23 removed outlier: 3.840A pdb=" N LYS D 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 42 through 53 removed outlier: 3.550A pdb=" N ARG D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 removed outlier: 4.089A pdb=" N ALA D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 4.946A pdb=" N ASP D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 141 removed outlier: 3.939A pdb=" N ILE D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.335A pdb=" N ILE D 145 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'E' and resid 14 through 17 Processing helix chain 'E' and resid 18 through 27 removed outlier: 3.772A pdb=" N TYR E 22 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU E 26 " --> pdb=" O TYR E 22 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.722A pdb=" N LYS E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 74 removed outlier: 4.097A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 104 removed outlier: 4.129A pdb=" N ASP E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Proline residue: E 85 - end of helix removed outlier: 3.719A pdb=" N TRP E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 101 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 146 removed outlier: 3.670A pdb=" N LYS E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'F' and resid 44 through 83 removed outlier: 3.960A pdb=" N LYS F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.713A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 110 through 135 removed outlier: 3.517A pdb=" N ALA F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 removed outlier: 3.923A pdb=" N LYS F 139 " --> pdb=" O SER F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'G' and resid 78 through 94 Processing helix chain 'H' and resid 78 through 94 Processing helix chain 'I' and resid 78 through 98 Processing helix chain 'J' and resid 78 through 97 removed outlier: 3.599A pdb=" N GLN J 97 " --> pdb=" O PHE J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 94 Processing helix chain 'L' and resid 78 through 95 removed outlier: 3.508A pdb=" N PHE L 93 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.984A pdb=" N VAL A 68 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 4.017A pdb=" N SER A 181 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 127 removed outlier: 3.779A pdb=" N GLN B 125 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.500A pdb=" N ARG B 206 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 435 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2182 1.33 - 1.45: 1673 1.45 - 1.57: 4450 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8348 Sorted by residual: bond pdb=" C ARG D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C GLU A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.523 1.570 -0.046 1.80e-02 3.09e+03 6.65e+00 bond pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.09e+00 bond pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 ... (remaining 8343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 10997 3.58 - 7.16: 225 7.16 - 10.74: 42 10.74 - 14.32: 5 14.32 - 17.90: 2 Bond angle restraints: 11271 Sorted by residual: angle pdb=" C THR A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C LYS D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA TYR A 45 " pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 113.90 123.83 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C ASP A 153 " pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " ideal model delta sigma weight residual 110.36 100.37 9.99 1.85e+00 2.92e-01 2.92e+01 angle pdb=" C ASP A 264 " pdb=" N GLU A 265 " pdb=" CA GLU A 265 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 ... (remaining 11266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4589 16.07 - 32.14: 371 32.14 - 48.21: 78 48.21 - 64.28: 1 64.28 - 80.34: 6 Dihedral angle restraints: 5045 sinusoidal: 1896 harmonic: 3149 Sorted by residual: dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta harmonic sigma weight residual -180.00 -139.12 -40.88 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N SER B 115 " pdb=" CA SER B 115 " ideal model delta harmonic sigma weight residual -180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA TYR B 113 " pdb=" C TYR B 113 " pdb=" N SER B 114 " pdb=" CA SER B 114 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 210 0.158 - 0.237: 40 0.237 - 0.316: 6 0.316 - 0.395: 2 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA TYR A 45 " pdb=" N TYR A 45 " pdb=" C TYR A 45 " pdb=" CB TYR A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1252 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 90 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C ASP D 90 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP D 90 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 91 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 46 " -0.034 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR F 46 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR F 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 46 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 46 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 46 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR F 46 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 46 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 45 " -0.035 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 45 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2080 2.78 - 3.31: 7828 3.31 - 3.84: 12670 3.84 - 4.37: 13537 4.37 - 4.90: 22438 Nonbonded interactions: 58553 Sorted by model distance: nonbonded pdb=" O ILE A 157 " pdb=" OG1 THR A 161 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 292 " pdb=" O LEU A 297 " model vdw 2.261 3.040 nonbonded pdb=" O PHE A 273 " pdb=" OG SER A 276 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR D 66 " pdb=" OD1 ASP F 67 " model vdw 2.314 3.040 nonbonded pdb=" O THR A 108 " pdb=" OH TYR A 132 " model vdw 2.318 3.040 ... (remaining 58548 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 144)) selection = (chain 'E' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or r \ esid 52 through 105 or (resid 106 through 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 through 144)) selection = (chain 'F' and (resid 24 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 105 or (resid 106 thr \ ough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 t \ hrough 110 or (resid 111 and (name N or name CA or name C or name O or name CB ) \ ) or resid 112 through 144)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 77 through 98) selection = (chain 'J' and resid 77 through 98) selection = (chain 'K' and (name N or name CA or name C or name O or name CB )) selection = (chain 'L' and resid 77 through 98) } 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=0.00 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: 4.310 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.009 0.082 8348 Z= 0.426 Angle : 1.315 17.897 11271 Z= 0.721 Chirality : 0.069 0.395 1255 Planarity : 0.007 0.073 1460 Dihedral : 12.355 80.344 2989 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.95 % Favored : 87.85 % Rotamer: Outliers : 1.10 % Allowed : 6.11 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -4.54 (0.20), residues: 1029 helix: -2.28 (0.16), residues: 582 sheet: -3.46 (0.43), residues: 84 loop : -3.95 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 24 TYR 0.066 0.005 TYR A 45 PHE 0.064 0.005 PHE D 31 TRP 0.026 0.004 TRP F 95 HIS 0.021 0.006 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.43 ( 8348) covalent geometry : angle 1.31470 / 0.72 (11271) hydrogen bonds : bond 0.16551 / 11.02 ( 435) hydrogen bonds : angle 7.28134 / 5.11 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 417 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 77 GLN cc_start: 0.9381 (mp10) cc_final: 0.9031 (mp10) REVERT: A 185 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7686 (ttmt) REVERT: A 201 TYR cc_start: 0.9084 (t80) cc_final: 0.8456 (t80) REVERT: A 241 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8345 (tppt) REVERT: A 244 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 248 TYR cc_start: 0.8663 (t80) cc_final: 0.8438 (t80) REVERT: A 259 GLU cc_start: 0.7944 (mp0) cc_final: 0.7744 (mp0) REVERT: A 303 TYR cc_start: 0.8184 (t80) cc_final: 0.7851 (t80) REVERT: A 306 GLU cc_start: 0.6681 (pt0) cc_final: 0.6439 (pt0) REVERT: B 18 LYS cc_start: 0.9060 (tmmm) cc_final: 0.8793 (ttpt) REVERT: B 47 ASP cc_start: 0.8620 (p0) cc_final: 0.8162 (p0) REVERT: B 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9250 (tp) REVERT: B 80 HIS cc_start: 0.8830 (t-90) cc_final: 0.8628 (t-90) REVERT: B 125 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 145 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0) REVERT: B 188 ASP cc_start: 0.8873 (p0) cc_final: 0.8222 (m-30) REVERT: B 250 ILE cc_start: 0.8450 (tp) cc_final: 0.8176 (tt) REVERT: D 25 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7588 (mpp-170) REVERT: D 38 TYR cc_start: 0.8652 (m-80) cc_final: 0.8447 (m-80) REVERT: D 47 ASP cc_start: 0.7655 (t0) cc_final: 0.7420 (t0) REVERT: D 75 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7705 (mmpt) REVERT: D 87 GLN cc_start: 0.9137 (mt0) cc_final: 0.8905 (mt0) REVERT: D 90 ASP cc_start: 0.7751 (t0) cc_final: 0.7465 (p0) REVERT: D 133 ASP cc_start: 0.8682 (t0) cc_final: 0.8318 (t70) REVERT: E 14 ILE cc_start: 0.8274 (mm) cc_final: 0.7958 (pt) REVERT: E 17 PHE cc_start: 0.9141 (m-80) cc_final: 0.8863 (m-10) REVERT: E 22 TYR cc_start: 0.8511 (t80) cc_final: 0.7942 (t80) REVERT: E 23 LYS cc_start: 0.9392 (tptp) cc_final: 0.9189 (tptt) REVERT: E 51 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7403 (tmt170) REVERT: E 86 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 90 ASP cc_start: 0.8850 (t0) cc_final: 0.8375 (m-30) REVERT: E 104 ILE cc_start: 0.8808 (mt) cc_final: 0.7932 (mm) REVERT: F 27 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7751 (tpt-90) REVERT: F 43 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8339 (mptt) REVERT: F 54 LYS cc_start: 0.6338 (tmmt) cc_final: 0.5470 (mttt) REVERT: F 57 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8380 (tm-30) REVERT: F 68 ASN cc_start: 0.8697 (t0) cc_final: 0.8437 (t0) REVERT: F 87 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8150 (tp-100) REVERT: F 91 LEU cc_start: 0.7608 (pp) cc_final: 0.6592 (pp) REVERT: F 123 PHE cc_start: 0.7056 (t80) cc_final: 0.6730 (t80) REVERT: F 125 VAL cc_start: 0.9406 (t) cc_final: 0.9038 (p) REVERT: F 143 LYS cc_start: 0.5689 (mppt) cc_final: 0.4090 (mmtt) outliers start: 9 outliers final: 2 residues processed: 420 average time/residue: 0.0890 time to fit residues: 49.6893 Evaluate side-chains 310 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS E 6 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130161 restraints weight = 18778.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132499 restraints weight = 9540.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133850 restraints weight = 5747.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134800 restraints weight = 4060.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135463 restraints weight = 3187.259| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8348 Z= 0.148 Angle : 0.769 12.088 11271 Z= 0.408 Chirality : 0.047 0.222 1255 Planarity : 0.005 0.049 1460 Dihedral : 6.599 36.183 1138 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.77 % Allowed : 17.36 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.60 (0.24), residues: 1029 helix: -0.42 (0.20), residues: 593 sheet: -3.26 (0.47), residues: 69 loop : -3.62 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.025 0.002 TYR A 45 PHE 0.026 0.002 PHE F 84 TRP 0.014 0.001 TRP F 95 HIS 0.004 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8348) covalent geometry : angle 0.76854 / 0.41 (11271) hydrogen bonds : bond 0.03945 / 2.56 ( 435) hydrogen bonds : angle 4.80446 / 3.29 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 26 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.7907 (ttp-170) REVERT: A 45 TYR cc_start: 0.8788 (p90) cc_final: 0.7403 (p90) REVERT: A 57 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 74 ARG cc_start: 0.6824 (mmp-170) cc_final: 0.6593 (tpt-90) REVERT: A 76 LYS cc_start: 0.8583 (pttt) cc_final: 0.8186 (ptmt) REVERT: A 185 LYS cc_start: 0.7622 (ttmt) cc_final: 0.6912 (tmtt) REVERT: A 189 ASN cc_start: 0.7009 (m-40) cc_final: 0.6695 (m-40) REVERT: A 214 ASN cc_start: 0.6535 (m110) cc_final: 0.6304 (m110) REVERT: A 248 TYR cc_start: 0.8485 (t80) cc_final: 0.8154 (t80) REVERT: A 259 GLU cc_start: 0.7646 (mp0) cc_final: 0.7178 (mp0) REVERT: A 303 TYR cc_start: 0.7788 (t80) cc_final: 0.7453 (t80) REVERT: B 38 GLN cc_start: 0.7865 (pm20) cc_final: 0.7358 (pt0) REVERT: B 188 ASP cc_start: 0.8604 (p0) cc_final: 0.8397 (m-30) REVERT: D 25 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7436 (mpp-170) REVERT: D 47 ASP cc_start: 0.7359 (t0) cc_final: 0.7154 (t0) REVERT: D 96 LEU cc_start: 0.7069 (pp) cc_final: 0.6570 (pp) REVERT: D 122 LEU cc_start: 0.9074 (pp) cc_final: 0.8654 (mp) REVERT: D 141 LEU cc_start: 0.8840 (mt) cc_final: 0.8527 (pp) REVERT: E 22 TYR cc_start: 0.8436 (t80) cc_final: 0.7809 (t80) REVERT: E 46 TYR cc_start: 0.9167 (t80) cc_final: 0.8632 (t80) REVERT: E 78 ASP cc_start: 0.8512 (m-30) cc_final: 0.7929 (t0) REVERT: E 86 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 27 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7631 (tpt-90) REVERT: F 43 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8300 (mptt) REVERT: F 54 LYS cc_start: 0.6738 (tmmt) cc_final: 0.6100 (mttt) REVERT: F 57 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8096 (tm-30) REVERT: F 78 ASP cc_start: 0.7832 (m-30) cc_final: 0.7517 (m-30) REVERT: F 87 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8029 (tp-100) REVERT: F 91 LEU cc_start: 0.7566 (pp) cc_final: 0.6570 (pp) REVERT: F 116 LEU cc_start: 0.9166 (mt) cc_final: 0.8891 (mt) REVERT: F 125 VAL cc_start: 0.9347 (t) cc_final: 0.8959 (t) REVERT: F 129 LYS cc_start: 0.9245 (pttp) cc_final: 0.9035 (mmtm) REVERT: F 143 LYS cc_start: 0.5649 (mppt) cc_final: 0.3675 (mmtt) outliers start: 39 outliers final: 20 residues processed: 371 average time/residue: 0.0888 time to fit residues: 44.0947 Evaluate side-chains 317 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128972 restraints weight = 18905.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131179 restraints weight = 9531.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132635 restraints weight = 5781.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133582 restraints weight = 4039.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133891 restraints weight = 3153.780| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8348 Z= 0.148 Angle : 0.749 10.858 11271 Z= 0.390 Chirality : 0.047 0.251 1255 Planarity : 0.004 0.041 1460 Dihedral : 5.938 35.435 1136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.60 % Allowed : 18.70 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1029 helix: 0.39 (0.21), residues: 596 sheet: -2.91 (0.50), residues: 69 loop : -3.53 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.030 0.002 TYR E 45 PHE 0.023 0.002 PHE E 74 TRP 0.014 0.001 TRP F 95 HIS 0.010 0.002 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8348) covalent geometry : angle 0.74875 / 0.39 (11271) hydrogen bonds : bond 0.03447 / 2.28 ( 435) hydrogen bonds : angle 4.46177 / 3.05 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2576 (ptt-90) cc_final: 0.2337 (ptt-90) REVERT: A 45 TYR cc_start: 0.8819 (p90) cc_final: 0.7920 (p90) REVERT: A 57 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 163 GLU cc_start: 0.8002 (tt0) cc_final: 0.7759 (tt0) REVERT: A 189 ASN cc_start: 0.7063 (m-40) cc_final: 0.6776 (m-40) REVERT: B 23 GLU cc_start: 0.8139 (pm20) cc_final: 0.7199 (pt0) REVERT: B 30 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8390 (mm) REVERT: B 188 ASP cc_start: 0.8618 (p0) cc_final: 0.8372 (m-30) REVERT: B 229 ASP cc_start: 0.7685 (t0) cc_final: 0.7482 (t0) REVERT: D 25 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7390 (mpp-170) REVERT: D 38 TYR cc_start: 0.8815 (m-80) cc_final: 0.8603 (m-80) REVERT: D 122 LEU cc_start: 0.9033 (pp) cc_final: 0.8628 (mp) REVERT: E 78 ASP cc_start: 0.8516 (m-30) cc_final: 0.7970 (t0) REVERT: F 27 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7606 (tpt-90) REVERT: F 41 ASN cc_start: 0.8880 (m110) cc_final: 0.8512 (m110) REVERT: F 54 LYS cc_start: 0.6761 (tmmt) cc_final: 0.6071 (mttt) REVERT: F 57 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8183 (tm-30) REVERT: F 87 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8008 (tp-100) REVERT: F 91 LEU cc_start: 0.7612 (pp) cc_final: 0.6624 (pp) REVERT: F 131 MET cc_start: 0.7301 (mmm) cc_final: 0.6974 (mmp) outliers start: 54 outliers final: 34 residues processed: 337 average time/residue: 0.0747 time to fit residues: 35.2248 Evaluate side-chains 333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 96 optimal weight: 9.9990 chunk 19 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.781 > 50:) chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 189 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131400 restraints weight = 19371.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133740 restraints weight = 9576.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134901 restraints weight = 5721.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136004 restraints weight = 4109.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136476 restraints weight = 3162.819| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8348 Z= 0.130 Angle : 0.736 9.587 11271 Z= 0.374 Chirality : 0.047 0.202 1255 Planarity : 0.004 0.034 1460 Dihedral : 5.607 34.422 1136 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.36 % Allowed : 21.27 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.26 (0.27), residues: 1029 helix: 0.78 (0.22), residues: 597 sheet: -2.45 (0.53), residues: 71 loop : -3.38 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 285 TYR 0.027 0.002 TYR E 45 PHE 0.023 0.002 PHE E 109 TRP 0.009 0.001 TRP D 77 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8348) covalent geometry : angle 0.73578 / 0.37 (11271) hydrogen bonds : bond 0.03146 / 2.08 ( 435) hydrogen bonds : angle 4.29517 / 2.93 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 316 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6249 (tt0) cc_final: 0.5833 (tt0) REVERT: A 45 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7914 (p90) REVERT: A 57 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 189 ASN cc_start: 0.7051 (m-40) cc_final: 0.6780 (m-40) REVERT: A 248 TYR cc_start: 0.8407 (t80) cc_final: 0.8080 (t80) REVERT: B 23 GLU cc_start: 0.8122 (pm20) cc_final: 0.7169 (pt0) REVERT: B 30 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 40 MET cc_start: 0.8676 (tpp) cc_final: 0.7476 (mtt) REVERT: B 188 ASP cc_start: 0.8567 (p0) cc_final: 0.8359 (m-30) REVERT: B 210 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7742 (tp-100) REVERT: D 25 ARG cc_start: 0.8080 (ttt180) cc_final: 0.7388 (mpp-170) REVERT: D 93 ARG cc_start: 0.7663 (mmp80) cc_final: 0.7408 (mmp80) REVERT: D 122 LEU cc_start: 0.9028 (pp) cc_final: 0.8608 (mp) REVERT: E 78 ASP cc_start: 0.8550 (m-30) cc_final: 0.8042 (t0) REVERT: E 104 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (mp) REVERT: E 145 ILE cc_start: 0.7184 (pt) cc_final: 0.6911 (mm) REVERT: F 27 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7588 (tpt-90) REVERT: F 54 LYS cc_start: 0.6842 (tmmt) cc_final: 0.6133 (mttt) REVERT: F 57 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8078 (tm-30) REVERT: F 87 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7987 (tp-100) REVERT: F 91 LEU cc_start: 0.7659 (pp) cc_final: 0.6629 (pp) REVERT: F 128 MET cc_start: 0.8623 (mmm) cc_final: 0.8373 (mmm) outliers start: 52 outliers final: 42 residues processed: 331 average time/residue: 0.0845 time to fit residues: 38.3241 Evaluate side-chains 333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 288 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 131 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133785 restraints weight = 19140.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136092 restraints weight = 9354.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137408 restraints weight = 5579.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138395 restraints weight = 3922.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138950 restraints weight = 3026.697| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8348 Z= 0.126 Angle : 0.732 9.318 11271 Z= 0.371 Chirality : 0.046 0.202 1255 Planarity : 0.004 0.046 1460 Dihedral : 5.310 32.873 1136 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.99 % Allowed : 22.74 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.04 (0.27), residues: 1029 helix: 0.90 (0.22), residues: 600 sheet: -1.85 (0.57), residues: 71 loop : -3.34 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.029 0.001 TYR E 45 PHE 0.026 0.002 PHE E 109 TRP 0.030 0.001 TRP E 95 HIS 0.006 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 8348) covalent geometry : angle 0.73181 / 0.37 (11271) hydrogen bonds : bond 0.03003 / 1.98 ( 435) hydrogen bonds : angle 4.13239 / 2.84 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.9025 (ttp-170) cc_final: 0.7921 (ttp-170) REVERT: A 37 GLU cc_start: 0.5665 (tt0) cc_final: 0.5277 (tt0) REVERT: A 45 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7841 (p90) REVERT: A 57 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 189 ASN cc_start: 0.6988 (m-40) cc_final: 0.6650 (m-40) REVERT: A 209 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (tpp) REVERT: A 248 TYR cc_start: 0.8381 (t80) cc_final: 0.8175 (t80) REVERT: B 30 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 40 MET cc_start: 0.8576 (tpp) cc_final: 0.7343 (mtt) REVERT: B 47 ASP cc_start: 0.8331 (p0) cc_final: 0.8027 (p0) REVERT: B 76 SER cc_start: 0.9346 (t) cc_final: 0.8923 (m) REVERT: B 130 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.7110 (t70) REVERT: D 25 ARG cc_start: 0.8075 (ttt180) cc_final: 0.7403 (mpp-170) REVERT: D 122 LEU cc_start: 0.9035 (pp) cc_final: 0.8578 (mp) REVERT: E 22 TYR cc_start: 0.8245 (t80) cc_final: 0.7872 (t80) REVERT: E 41 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.7007 (t0) REVERT: E 46 TYR cc_start: 0.9177 (t80) cc_final: 0.8759 (t80) REVERT: E 52 LEU cc_start: 0.9225 (tp) cc_final: 0.8887 (tt) REVERT: E 78 ASP cc_start: 0.8513 (m-30) cc_final: 0.8075 (t0) REVERT: E 145 ILE cc_start: 0.7167 (pt) cc_final: 0.6854 (mm) REVERT: F 27 ARG cc_start: 0.8201 (ptp90) cc_final: 0.7582 (tpt-90) REVERT: F 54 LYS cc_start: 0.6790 (tmmt) cc_final: 0.6187 (mttt) REVERT: F 57 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8068 (tm-30) REVERT: F 87 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7977 (tp-100) REVERT: F 91 LEU cc_start: 0.7632 (pp) cc_final: 0.6654 (pp) REVERT: F 128 MET cc_start: 0.8699 (mmm) cc_final: 0.8389 (mmm) REVERT: F 131 MET cc_start: 0.7930 (mmp) cc_final: 0.7281 (mmm) outliers start: 49 outliers final: 31 residues processed: 337 average time/residue: 0.0834 time to fit residues: 38.4777 Evaluate side-chains 334 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126675 restraints weight = 19071.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128848 restraints weight = 9490.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130158 restraints weight = 5776.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131052 restraints weight = 4096.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131628 restraints weight = 3212.882| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8348 Z= 0.194 Angle : 0.796 10.257 11271 Z= 0.415 Chirality : 0.050 0.224 1255 Planarity : 0.004 0.049 1460 Dihedral : 5.774 38.655 1136 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.09 % Allowed : 24.33 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.02 (0.27), residues: 1029 helix: 0.99 (0.22), residues: 598 sheet: -2.29 (0.55), residues: 71 loop : -3.34 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 15 TYR 0.038 0.002 TYR F 38 PHE 0.032 0.003 PHE F 74 TRP 0.025 0.002 TRP E 95 HIS 0.006 0.002 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8348) covalent geometry : angle 0.79569 / 0.41 (11271) hydrogen bonds : bond 0.03586 / 2.39 ( 435) hydrogen bonds : angle 4.31710 / 2.99 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5403 (tt0) cc_final: 0.4729 (tt0) REVERT: A 45 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.7921 (p90) REVERT: A 57 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 77 GLN cc_start: 0.9154 (mp10) cc_final: 0.8935 (mp10) REVERT: A 209 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: A 248 TYR cc_start: 0.8500 (t80) cc_final: 0.8218 (t80) REVERT: A 321 GLU cc_start: 0.8454 (tp30) cc_final: 0.7373 (tp30) REVERT: B 30 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 97 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 130 HIS cc_start: 0.7459 (OUTLIER) cc_final: 0.6966 (t70) REVERT: B 188 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5353 (m-30) REVERT: B 222 GLN cc_start: 0.8588 (tp40) cc_final: 0.8386 (tp40) REVERT: B 244 LYS cc_start: 0.7459 (mptt) cc_final: 0.7189 (mmtt) REVERT: D 25 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7416 (mpp-170) REVERT: D 37 ASP cc_start: 0.8603 (p0) cc_final: 0.8401 (p0) REVERT: D 40 THR cc_start: 0.9226 (p) cc_final: 0.9008 (m) REVERT: D 67 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: D 122 LEU cc_start: 0.9098 (pp) cc_final: 0.8693 (mp) REVERT: E 46 TYR cc_start: 0.9195 (t80) cc_final: 0.8835 (t80) REVERT: E 78 ASP cc_start: 0.8497 (m-30) cc_final: 0.8081 (t0) REVERT: F 27 ARG cc_start: 0.8378 (ptp90) cc_final: 0.7533 (tpt-90) REVERT: F 51 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8305 (ttm-80) REVERT: F 54 LYS cc_start: 0.6764 (tmmt) cc_final: 0.6119 (mttt) REVERT: F 57 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 67 ASP cc_start: 0.8732 (m-30) cc_final: 0.8473 (m-30) REVERT: F 87 GLN cc_start: 0.8443 (tp-100) cc_final: 0.7975 (tp-100) REVERT: F 91 LEU cc_start: 0.7953 (pp) cc_final: 0.7087 (pp) REVERT: F 128 MET cc_start: 0.8804 (mmm) cc_final: 0.8550 (mmm) outliers start: 58 outliers final: 42 residues processed: 332 average time/residue: 0.0816 time to fit residues: 37.4966 Evaluate side-chains 338 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128637 restraints weight = 19235.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130911 restraints weight = 9362.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132381 restraints weight = 5591.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133179 restraints weight = 3860.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133772 restraints weight = 3043.971| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8348 Z= 0.160 Angle : 0.774 9.990 11271 Z= 0.399 Chirality : 0.049 0.223 1255 Planarity : 0.004 0.067 1460 Dihedral : 5.590 36.597 1136 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 6.72 % Allowed : 25.67 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.03 (0.27), residues: 1029 helix: 0.95 (0.22), residues: 605 sheet: -2.22 (0.56), residues: 71 loop : -3.38 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 15 TYR 0.029 0.002 TYR E 45 PHE 0.029 0.002 PHE F 74 TRP 0.020 0.002 TRP E 95 HIS 0.006 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8348) covalent geometry : angle 0.77442 / 0.40 (11271) hydrogen bonds : bond 0.03230 / 2.11 ( 435) hydrogen bonds : angle 4.27743 / 2.97 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8686 (tpp) cc_final: 0.8371 (tpp) REVERT: A 37 GLU cc_start: 0.5068 (tt0) cc_final: 0.4092 (tt0) REVERT: A 45 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.7669 (p90) REVERT: A 55 PHE cc_start: 0.8655 (m-80) cc_final: 0.8014 (m-80) REVERT: A 74 ARG cc_start: 0.3716 (tpt-90) cc_final: 0.3358 (tpt-90) REVERT: A 242 ILE cc_start: 0.9291 (tt) cc_final: 0.9016 (tt) REVERT: A 248 TYR cc_start: 0.8495 (t80) cc_final: 0.8147 (t80) REVERT: A 321 GLU cc_start: 0.8514 (tp30) cc_final: 0.8107 (tp30) REVERT: B 18 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8848 (ttpt) REVERT: B 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 40 MET cc_start: 0.8532 (tpp) cc_final: 0.7544 (mtt) REVERT: B 130 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6878 (t70) REVERT: B 145 ASN cc_start: 0.7737 (p0) cc_final: 0.7429 (p0) REVERT: B 188 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5399 (m-30) REVERT: B 244 LYS cc_start: 0.7412 (mptt) cc_final: 0.7117 (mmtt) REVERT: D 25 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7444 (mpp-170) REVERT: D 75 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7746 (mmpt) REVERT: D 93 ARG cc_start: 0.7444 (mmp80) cc_final: 0.6954 (mmp80) REVERT: D 122 LEU cc_start: 0.9037 (pp) cc_final: 0.8584 (mp) REVERT: E 46 TYR cc_start: 0.9182 (t80) cc_final: 0.8856 (t80) REVERT: E 52 LEU cc_start: 0.9309 (tp) cc_final: 0.9065 (tt) REVERT: E 69 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8559 (tm-30) REVERT: E 78 ASP cc_start: 0.8550 (m-30) cc_final: 0.8121 (t0) REVERT: E 145 ILE cc_start: 0.7323 (pt) cc_final: 0.6969 (mm) REVERT: F 27 ARG cc_start: 0.8403 (ptp90) cc_final: 0.7493 (tpt-90) REVERT: F 54 LYS cc_start: 0.6787 (tmmt) cc_final: 0.6086 (mttt) REVERT: F 57 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8189 (tm-30) REVERT: F 87 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7896 (tp-100) REVERT: F 91 LEU cc_start: 0.7887 (pp) cc_final: 0.6994 (pp) REVERT: F 131 MET cc_start: 0.7937 (mmp) cc_final: 0.7280 (mmm) outliers start: 55 outliers final: 42 residues processed: 320 average time/residue: 0.0821 time to fit residues: 36.4249 Evaluate side-chains 332 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133131 restraints weight = 19043.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135416 restraints weight = 9302.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136736 restraints weight = 5527.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137694 restraints weight = 3868.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138113 restraints weight = 2993.368| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8348 Z= 0.134 Angle : 0.775 9.909 11271 Z= 0.390 Chirality : 0.046 0.198 1255 Planarity : 0.004 0.071 1460 Dihedral : 5.249 33.909 1136 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.89 % Allowed : 28.12 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.28), residues: 1029 helix: 1.10 (0.22), residues: 602 sheet: -1.85 (0.58), residues: 71 loop : -3.27 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 15 TYR 0.019 0.001 TYR D 66 PHE 0.023 0.001 PHE F 74 TRP 0.017 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8348) covalent geometry : angle 0.77526 / 0.39 (11271) hydrogen bonds : bond 0.02972 / 1.94 ( 435) hydrogen bonds : angle 4.17954 / 2.90 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8753 (tpp) cc_final: 0.8450 (tpp) REVERT: A 37 GLU cc_start: 0.4756 (tt0) cc_final: 0.3596 (tt0) REVERT: A 45 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7752 (p90) REVERT: A 55 PHE cc_start: 0.8608 (m-80) cc_final: 0.7927 (m-80) REVERT: A 74 ARG cc_start: 0.3629 (tpt-90) cc_final: 0.3276 (tpt-90) REVERT: A 242 ILE cc_start: 0.9241 (tt) cc_final: 0.9011 (tt) REVERT: A 248 TYR cc_start: 0.8421 (t80) cc_final: 0.8131 (t80) REVERT: A 321 GLU cc_start: 0.8464 (tp30) cc_final: 0.8008 (tp30) REVERT: B 30 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 40 MET cc_start: 0.8436 (tpp) cc_final: 0.7416 (mtt) REVERT: B 76 SER cc_start: 0.9355 (t) cc_final: 0.8965 (m) REVERT: B 123 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 130 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6671 (t70) REVERT: B 244 LYS cc_start: 0.7406 (mptt) cc_final: 0.7094 (mmtt) REVERT: D 25 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7454 (mpp-170) REVERT: D 75 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7649 (mmpt) REVERT: D 122 LEU cc_start: 0.9049 (pp) cc_final: 0.8575 (mp) REVERT: E 20 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7323 (tm-30) REVERT: E 41 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.6981 (t0) REVERT: E 46 TYR cc_start: 0.9011 (t80) cc_final: 0.8677 (t80) REVERT: E 78 ASP cc_start: 0.8488 (m-30) cc_final: 0.8087 (t0) REVERT: E 145 ILE cc_start: 0.7301 (pt) cc_final: 0.6914 (mm) REVERT: F 27 ARG cc_start: 0.8348 (ptp90) cc_final: 0.7496 (tpt-90) REVERT: F 43 LYS cc_start: 0.5875 (mptt) cc_final: 0.5555 (mptt) REVERT: F 54 LYS cc_start: 0.6791 (tmmt) cc_final: 0.6178 (mttt) REVERT: F 57 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8120 (tm-30) REVERT: F 87 GLN cc_start: 0.8338 (tp-100) cc_final: 0.7878 (tp-100) outliers start: 40 outliers final: 28 residues processed: 315 average time/residue: 0.0803 time to fit residues: 35.1262 Evaluate side-chains 314 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 131 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131020 restraints weight = 19018.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133261 restraints weight = 9310.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134618 restraints weight = 5576.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135544 restraints weight = 3907.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136158 restraints weight = 3057.111| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8348 Z= 0.149 Angle : 0.797 10.999 11271 Z= 0.402 Chirality : 0.047 0.206 1255 Planarity : 0.004 0.069 1460 Dihedral : 5.270 34.924 1136 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.38 % Allowed : 28.61 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.27), residues: 1029 helix: 1.15 (0.22), residues: 601 sheet: -1.66 (0.60), residues: 71 loop : -3.31 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 15 TYR 0.017 0.002 TYR A 45 PHE 0.018 0.002 PHE F 134 TRP 0.016 0.001 TRP E 95 HIS 0.006 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8348) covalent geometry : angle 0.79680 / 0.40 (11271) hydrogen bonds : bond 0.03090 / 2.01 ( 435) hydrogen bonds : angle 4.18370 / 2.89 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8764 (tpp) cc_final: 0.8474 (tpp) REVERT: A 37 GLU cc_start: 0.4872 (tt0) cc_final: 0.3785 (tt0) REVERT: A 45 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7891 (p90) REVERT: A 166 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6407 (pp20) REVERT: A 242 ILE cc_start: 0.9248 (tt) cc_final: 0.8999 (tt) REVERT: A 248 TYR cc_start: 0.8505 (t80) cc_final: 0.8196 (t80) REVERT: A 295 TYR cc_start: 0.8318 (m-10) cc_final: 0.8058 (m-80) REVERT: A 321 GLU cc_start: 0.8551 (tp30) cc_final: 0.8092 (tp30) REVERT: B 18 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8884 (ttpt) REVERT: B 23 GLU cc_start: 0.7995 (pm20) cc_final: 0.6952 (pt0) REVERT: B 30 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8356 (mm) REVERT: B 40 MET cc_start: 0.8448 (tpp) cc_final: 0.7308 (mtt) REVERT: B 145 ASN cc_start: 0.7616 (p0) cc_final: 0.7322 (p0) REVERT: B 244 LYS cc_start: 0.7453 (mptt) cc_final: 0.7148 (mmtt) REVERT: D 25 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7452 (mpp-170) REVERT: D 75 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7729 (mmpt) REVERT: D 122 LEU cc_start: 0.9003 (pp) cc_final: 0.8550 (mp) REVERT: E 20 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7350 (tm-30) REVERT: E 46 TYR cc_start: 0.9007 (t80) cc_final: 0.8749 (t80) REVERT: E 69 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8486 (tm-30) REVERT: E 145 ILE cc_start: 0.7290 (pt) cc_final: 0.6900 (mm) REVERT: F 27 ARG cc_start: 0.8368 (ptp90) cc_final: 0.7484 (tpt-90) REVERT: F 54 LYS cc_start: 0.6811 (tmmt) cc_final: 0.6115 (mttt) REVERT: F 57 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8162 (tm-30) REVERT: F 87 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7821 (tp-100) REVERT: F 131 MET cc_start: 0.8191 (mmp) cc_final: 0.7299 (mmm) outliers start: 44 outliers final: 34 residues processed: 309 average time/residue: 0.0785 time to fit residues: 33.6956 Evaluate side-chains 320 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.155134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132562 restraints weight = 19118.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134840 restraints weight = 9291.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136262 restraints weight = 5537.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137100 restraints weight = 3820.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137674 restraints weight = 3003.148| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8348 Z= 0.142 Angle : 0.823 11.284 11271 Z= 0.414 Chirality : 0.048 0.210 1255 Planarity : 0.004 0.070 1460 Dihedral : 5.197 33.888 1136 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.01 % Allowed : 30.07 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.27), residues: 1029 helix: 1.15 (0.22), residues: 600 sheet: -1.36 (0.61), residues: 71 loop : -3.34 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 15 TYR 0.017 0.001 TYR A 45 PHE 0.021 0.002 PHE F 74 TRP 0.015 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8348) covalent geometry : angle 0.82285 / 0.41 (11271) hydrogen bonds : bond 0.03080 / 2.00 ( 435) hydrogen bonds : angle 4.28882 / 3.00 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8717 (tpp) cc_final: 0.8424 (tpp) REVERT: A 45 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7963 (p90) REVERT: A 55 PHE cc_start: 0.8780 (m-80) cc_final: 0.7996 (m-80) REVERT: A 74 ARG cc_start: 0.3728 (tpt-90) cc_final: 0.3370 (tpt-90) REVERT: A 166 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: A 248 TYR cc_start: 0.8512 (t80) cc_final: 0.8231 (t80) REVERT: A 295 TYR cc_start: 0.8254 (m-10) cc_final: 0.8007 (m-80) REVERT: A 321 GLU cc_start: 0.8542 (tp30) cc_final: 0.8090 (tp30) REVERT: B 18 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8862 (ttpt) REVERT: B 30 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8337 (mm) REVERT: B 40 MET cc_start: 0.8375 (tpp) cc_final: 0.7282 (mtt) REVERT: B 123 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 145 ASN cc_start: 0.7488 (p0) cc_final: 0.7133 (p0) REVERT: B 244 LYS cc_start: 0.7423 (mptt) cc_final: 0.7216 (tptt) REVERT: D 25 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7449 (mpp-170) REVERT: D 53 SER cc_start: 0.9107 (m) cc_final: 0.8697 (t) REVERT: D 75 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7628 (mmpt) REVERT: D 122 LEU cc_start: 0.9017 (pp) cc_final: 0.8563 (mp) REVERT: D 141 LEU cc_start: 0.8617 (pp) cc_final: 0.8259 (mt) REVERT: E 20 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7330 (tm-30) REVERT: E 41 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.6976 (t0) REVERT: E 145 ILE cc_start: 0.6967 (pt) cc_final: 0.6624 (mm) REVERT: F 27 ARG cc_start: 0.8351 (ptp90) cc_final: 0.7532 (tpt-90) REVERT: F 54 LYS cc_start: 0.6781 (tmmt) cc_final: 0.6161 (mttt) REVERT: F 57 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 87 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7803 (tp-100) outliers start: 41 outliers final: 31 residues processed: 295 average time/residue: 0.0818 time to fit residues: 33.2724 Evaluate side-chains 308 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127344 restraints weight = 19227.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129495 restraints weight = 9647.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130875 restraints weight = 5852.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131678 restraints weight = 4110.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132255 restraints weight = 3255.571| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8348 Z= 0.186 Angle : 0.857 11.266 11271 Z= 0.438 Chirality : 0.050 0.240 1255 Planarity : 0.005 0.076 1460 Dihedral : 5.562 37.851 1136 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.38 % Allowed : 29.71 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.27), residues: 1029 helix: 1.12 (0.22), residues: 599 sheet: -1.53 (0.56), residues: 81 loop : -3.47 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 15 TYR 0.025 0.002 TYR A 45 PHE 0.021 0.002 PHE E 11 TRP 0.014 0.002 TRP E 95 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 8348) covalent geometry : angle 0.85745 / 0.44 (11271) hydrogen bonds : bond 0.03527 / 2.31 ( 435) hydrogen bonds : angle 4.45209 / 3.11 ( 1278) =============================================================================== Job complete usr+sys time: 2000.79 seconds wall clock time: 34 minutes 51.78 seconds (2091.78 seconds total)