Starting phenix.real_space_refine on Wed Sep 17 10:15:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iac_4435/09_2025/6iac_4435.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iac_4435/09_2025/6iac_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_2025/6iac_4435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2025/6iac_4435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2025/6iac_4435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iac_4435/09_2025/6iac_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-2.0-5805/lib/python3.9/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: 2.14, per 1000 atoms: 0.26 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: 0.72 Conformation dependent library (CDL) restraints added in 418.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 1.16 Time building geometry restraints manager: 0.94 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: 6.010 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 aren 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 covalent geometry : bond 0.00943 ( 8348) covalent geometry : angle 1.31470 (11271) hydrogen bonds : bond 0.16551 ( 435) hydrogen bonds : angle 7.28134 ( 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 : 0.347 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: 0.7958 (tm-30) REVERT: A 248 TYR cc_start: 0.8663 (t80) cc_final: 0.8438 (t80) REVERT: A 303 TYR cc_start: 0.8185 (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: 0.6593 (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: 0.1121 time to fit residues: 61.5877 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 : 0.343 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3879 r_free = 0.3879 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130187 restraints weight = 18749.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132476 restraints weight = 9329.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133850 restraints weight = 5669.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134784 restraints weight = 3994.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135407 restraints weight = 3139.844| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8348 Z= 0.148 Angle : 0.770 12.181 11271 Z= 0.409 Chirality : 0.047 0.223 1255 Planarity : 0.005 0.054 1460 Dihedral : 6.588 36.153 1138 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.13 % Allowed : 16.75 % Favored : 78.12 % 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 aren not related in a simple way. whole: -2.57 (0.24), residues: 1029 helix: -0.38 (0.20), residues: 593 sheet: -3.25 (0.47), residues: 69 loop : -3.62 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 285 TYR 0.024 0.002 TYR A 45 PHE 0.026 0.002 PHE F 84 TRP 0.014 0.001 TRP F 95 HIS 0.005 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8348) covalent geometry : angle 0.77011 (11271) hydrogen bonds : bond 0.03930 ( 435) hydrogen bonds : angle 4.82360 ( 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 399 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 26 ARG cc_start: 0.9088 (ttp-170) cc_final: 0.7899 (ttp-170) REVERT: A 45 TYR cc_start: 0.8794 (p90) cc_final: 0.7385 (p90) REVERT: A 57 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 74 ARG cc_start: 0.6832 (mmp-170) cc_final: 0.6607 (tpt-90) REVERT: A 76 LYS cc_start: 0.8584 (pttt) cc_final: 0.8178 (ptmt) REVERT: A 185 LYS cc_start: 0.7621 (ttmt) cc_final: 0.6908 (tmtt) REVERT: A 189 ASN cc_start: 0.7019 (m-40) cc_final: 0.6702 (m-40) REVERT: A 214 ASN cc_start: 0.6484 (m110) cc_final: 0.6257 (m110) REVERT: A 248 TYR cc_start: 0.8487 (t80) cc_final: 0.8150 (t80) REVERT: A 259 GLU cc_start: 0.7528 (mp0) cc_final: 0.7326 (mp0) REVERT: A 303 TYR cc_start: 0.7788 (t80) cc_final: 0.7453 (t80) REVERT: B 30 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 38 GLN cc_start: 0.7839 (pm20) cc_final: 0.7284 (pt0) REVERT: B 188 ASP cc_start: 0.8618 (p0) cc_final: 0.8372 (m-30) REVERT: B 245 LYS cc_start: 0.8268 (mttt) cc_final: 0.8067 (mttt) REVERT: D 25 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7444 (mpp-170) REVERT: D 96 LEU cc_start: 0.7058 (pp) cc_final: 0.6557 (pp) REVERT: D 122 LEU cc_start: 0.9078 (pp) cc_final: 0.8658 (mp) REVERT: D 141 LEU cc_start: 0.8829 (mt) cc_final: 0.8519 (pp) REVERT: E 22 TYR cc_start: 0.8448 (t80) cc_final: 0.7824 (t80) REVERT: E 46 TYR cc_start: 0.9162 (t80) cc_final: 0.8550 (t80) REVERT: E 78 ASP cc_start: 0.8516 (m-30) cc_final: 0.7930 (t0) REVERT: E 86 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 27 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7627 (tpt-90) REVERT: F 43 LYS cc_start: 0.8557 (mtpm) cc_final: 0.8322 (mptt) REVERT: F 54 LYS cc_start: 0.6738 (tmmt) cc_final: 0.6122 (mttt) REVERT: F 57 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 75 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8350 (tptp) REVERT: F 78 ASP cc_start: 0.7826 (m-30) cc_final: 0.7607 (m-30) REVERT: F 87 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8019 (tp-100) REVERT: F 91 LEU cc_start: 0.7562 (pp) cc_final: 0.6560 (pp) REVERT: F 116 LEU cc_start: 0.9201 (mt) cc_final: 0.8931 (mt) REVERT: F 125 VAL cc_start: 0.9346 (t) cc_final: 0.8959 (t) REVERT: F 129 LYS cc_start: 0.9247 (pttp) cc_final: 0.9040 (mmtm) REVERT: F 143 LYS cc_start: 0.5641 (mppt) cc_final: 0.3683 (mmtt) outliers start: 42 outliers final: 21 residues processed: 375 average time/residue: 0.1013 time to fit residues: 50.4944 Evaluate side-chains 329 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain A residue 256 VAL 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 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: 0.7980 chunk 91 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3891 r_free = 0.3891 target = 0.154952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131830 restraints weight = 18940.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134056 restraints weight = 9552.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135391 restraints weight = 5836.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136402 restraints weight = 4124.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136896 restraints weight = 3210.438| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4260 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= 0.131 Angle : 0.735 10.382 11271 Z= 0.380 Chirality : 0.046 0.234 1255 Planarity : 0.004 0.041 1460 Dihedral : 5.745 33.567 1136 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.62 % Allowed : 19.80 % Favored : 74.57 % 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 aren not related in a simple way. whole: -1.69 (0.26), residues: 1029 helix: 0.41 (0.21), residues: 599 sheet: -2.82 (0.51), residues: 69 loop : -3.50 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.022 0.002 TYR E 45 PHE 0.021 0.002 PHE E 74 TRP 0.011 0.001 TRP F 95 HIS 0.020 0.003 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8348) covalent geometry : angle 0.73509 (11271) hydrogen bonds : bond 0.03286 ( 435) hydrogen bonds : angle 4.37372 ( 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 365 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2309 (ptt-90) cc_final: 0.2078 (ptt-90) REVERT: A 45 TYR cc_start: 0.8725 (p90) cc_final: 0.7651 (p90) REVERT: A 57 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8228 (tm-30) REVERT: A 163 GLU cc_start: 0.7923 (tt0) cc_final: 0.7683 (tt0) REVERT: A 185 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6442 (tmtt) REVERT: A 189 ASN cc_start: 0.6861 (m-40) cc_final: 0.6551 (m-40) REVERT: A 248 TYR cc_start: 0.8419 (t80) cc_final: 0.8190 (t80) REVERT: B 23 GLU cc_start: 0.8124 (pm20) cc_final: 0.7207 (pt0) REVERT: B 188 ASP cc_start: 0.8595 (p0) cc_final: 0.8330 (m-30) REVERT: B 245 LYS cc_start: 0.8240 (mttt) cc_final: 0.7996 (mttt) REVERT: D 25 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7370 (mpp-170) REVERT: D 38 TYR cc_start: 0.8800 (m-80) cc_final: 0.8503 (m-80) REVERT: D 122 LEU cc_start: 0.9044 (pp) cc_final: 0.8655 (mp) REVERT: E 46 TYR cc_start: 0.9225 (t80) cc_final: 0.9022 (t80) REVERT: E 78 ASP cc_start: 0.8540 (m-30) cc_final: 0.8016 (t0) REVERT: F 27 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7637 (tpt-90) REVERT: F 41 ASN cc_start: 0.8789 (m110) cc_final: 0.8448 (m110) REVERT: F 54 LYS cc_start: 0.6777 (tmmt) cc_final: 0.6081 (mttm) REVERT: F 57 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 78 ASP cc_start: 0.7527 (m-30) cc_final: 0.7318 (m-30) REVERT: F 87 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7975 (tp-100) REVERT: F 91 LEU cc_start: 0.7567 (pp) cc_final: 0.6532 (pp) REVERT: F 128 MET cc_start: 0.8674 (mmm) cc_final: 0.8446 (mmm) outliers start: 46 outliers final: 29 residues processed: 337 average time/residue: 0.0926 time to fit residues: 42.8476 Evaluate side-chains 330 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 51 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 154 ILE Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 10 ASP 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 80 LEU 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 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: 9.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.0020 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 145 ASN B 189 ASN B 210 GLN F 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132399 restraints weight = 19346.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134674 restraints weight = 9546.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135993 restraints weight = 5761.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136947 restraints weight = 4056.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137508 restraints weight = 3174.377| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8348 Z= 0.130 Angle : 0.731 9.316 11271 Z= 0.372 Chirality : 0.046 0.198 1255 Planarity : 0.004 0.033 1460 Dihedral : 5.486 33.762 1136 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.75 % Allowed : 21.76 % Favored : 72.49 % 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 aren not related in a simple way. whole: -1.24 (0.27), residues: 1029 helix: 0.80 (0.22), residues: 597 sheet: -2.44 (0.54), residues: 71 loop : -3.38 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.021 0.001 TYR F 112 PHE 0.022 0.002 PHE E 109 TRP 0.010 0.001 TRP F 95 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8348) covalent geometry : angle 0.73076 (11271) hydrogen bonds : bond 0.03137 ( 435) hydrogen bonds : angle 4.22898 ( 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: 47 poor density : 321 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.9048 (ttp-170) cc_final: 0.7944 (ttp-170) REVERT: A 37 GLU cc_start: 0.6276 (tt0) cc_final: 0.5885 (tt0) REVERT: A 45 TYR cc_start: 0.8773 (p90) cc_final: 0.8311 (p90) REVERT: A 57 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 163 GLU cc_start: 0.7909 (tt0) cc_final: 0.7697 (tt0) REVERT: A 189 ASN cc_start: 0.7009 (m-40) cc_final: 0.6725 (m-40) REVERT: B 23 GLU cc_start: 0.8104 (pm20) cc_final: 0.7106 (pt0) REVERT: B 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 40 MET cc_start: 0.8646 (tpp) cc_final: 0.7478 (mtt) REVERT: B 125 GLN cc_start: 0.8260 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 188 ASP cc_start: 0.8576 (p0) cc_final: 0.8369 (m-30) REVERT: B 245 LYS cc_start: 0.8219 (mttt) cc_final: 0.7923 (mttt) REVERT: D 19 ASP cc_start: 0.7728 (p0) cc_final: 0.7516 (p0) REVERT: D 25 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7397 (mpp-170) REVERT: D 93 ARG cc_start: 0.7646 (mmp80) cc_final: 0.7240 (mmp80) REVERT: D 122 LEU cc_start: 0.9026 (pp) cc_final: 0.8614 (mp) REVERT: E 22 TYR cc_start: 0.8259 (t80) cc_final: 0.7859 (t80) REVERT: E 52 LEU cc_start: 0.9254 (tp) cc_final: 0.8862 (tt) REVERT: E 78 ASP cc_start: 0.8545 (m-30) cc_final: 0.8050 (t0) REVERT: E 145 ILE cc_start: 0.7189 (pt) cc_final: 0.6888 (mm) REVERT: F 27 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7583 (tpt-90) REVERT: F 41 ASN cc_start: 0.8834 (m110) cc_final: 0.8558 (m110) REVERT: F 54 LYS cc_start: 0.6796 (tmmt) cc_final: 0.6105 (mttt) REVERT: F 57 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8094 (tm-30) REVERT: F 87 GLN cc_start: 0.8469 (tp-100) cc_final: 0.7990 (tp-100) REVERT: F 91 LEU cc_start: 0.7654 (pp) cc_final: 0.6623 (pp) REVERT: F 128 MET cc_start: 0.8557 (mmm) cc_final: 0.8241 (mmm) outliers start: 47 outliers final: 37 residues processed: 338 average time/residue: 0.0968 time to fit residues: 44.2066 Evaluate side-chains 333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 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 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 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 55 LEU 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 141 LEU 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: 0.0670 chunk 62 optimal weight: 0.0010 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136043 restraints weight = 19166.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138410 restraints weight = 9384.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139750 restraints weight = 5534.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140658 restraints weight = 3843.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141071 restraints weight = 2994.827| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8348 Z= 0.125 Angle : 0.726 8.984 11271 Z= 0.368 Chirality : 0.046 0.205 1255 Planarity : 0.004 0.045 1460 Dihedral : 5.172 31.404 1136 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.52 % Allowed : 24.08 % Favored : 71.39 % 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 aren not related in a simple way. whole: -0.96 (0.27), residues: 1029 helix: 0.99 (0.22), residues: 597 sheet: -1.87 (0.56), residues: 71 loop : -3.31 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 285 TYR 0.025 0.001 TYR D 66 PHE 0.038 0.002 PHE D 109 TRP 0.025 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8348) covalent geometry : angle 0.72554 (11271) hydrogen bonds : bond 0.02953 ( 435) hydrogen bonds : angle 4.06976 ( 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 368 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 331 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.7885 (ttp-170) REVERT: A 37 GLU cc_start: 0.5557 (tt0) cc_final: 0.5190 (tt0) REVERT: A 45 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7411 (p90) REVERT: A 55 PHE cc_start: 0.8432 (m-80) cc_final: 0.7990 (m-10) REVERT: A 155 GLU cc_start: 0.8119 (tp30) cc_final: 0.7693 (tp30) REVERT: A 160 TYR cc_start: 0.8574 (m-80) cc_final: 0.8264 (m-80) REVERT: A 248 TYR cc_start: 0.8410 (t80) cc_final: 0.8158 (t80) REVERT: B 30 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8236 (mm) REVERT: B 40 MET cc_start: 0.8520 (tpp) cc_final: 0.7357 (mtt) REVERT: B 47 ASP cc_start: 0.8268 (p0) cc_final: 0.7995 (p0) REVERT: B 76 SER cc_start: 0.9309 (t) cc_final: 0.8989 (m) REVERT: D 19 ASP cc_start: 0.7745 (p0) cc_final: 0.7481 (p0) REVERT: D 25 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7422 (mpp-170) REVERT: D 122 LEU cc_start: 0.9027 (pp) cc_final: 0.8582 (mp) REVERT: E 41 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.6991 (t0) REVERT: E 78 ASP cc_start: 0.8518 (m-30) cc_final: 0.8092 (t0) REVERT: E 145 ILE cc_start: 0.7116 (pt) cc_final: 0.6807 (mm) REVERT: F 27 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7569 (tpt-90) REVERT: F 41 ASN cc_start: 0.8718 (m110) cc_final: 0.8435 (m110) REVERT: F 43 LYS cc_start: 0.5634 (mptt) cc_final: 0.5424 (mptt) REVERT: F 54 LYS cc_start: 0.6787 (tmmt) cc_final: 0.6207 (mttt) REVERT: F 57 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8024 (tm-30) REVERT: F 87 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7958 (tp-100) REVERT: F 91 LEU cc_start: 0.7579 (pp) cc_final: 0.6438 (pp) REVERT: F 128 MET cc_start: 0.8584 (mmm) cc_final: 0.8257 (mmm) REVERT: F 143 LYS cc_start: 0.5766 (mppt) cc_final: 0.3574 (mmtt) outliers start: 37 outliers final: 23 residues processed: 346 average time/residue: 0.0969 time to fit residues: 45.4177 Evaluate side-chains 316 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 45 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 148 ILE Chi-restraints excluded: chain A residue 180 PHE 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 324 ASP 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 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 67 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 79 ASP 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 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.0970 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3915 r_free = 0.3915 target = 0.156943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133979 restraints weight = 19142.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136262 restraints weight = 9549.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137542 restraints weight = 5715.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138456 restraints weight = 4051.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138946 restraints weight = 3150.775| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8348 Z= 0.134 Angle : 0.757 10.848 11271 Z= 0.383 Chirality : 0.048 0.240 1255 Planarity : 0.004 0.040 1460 Dihedral : 5.186 32.847 1136 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.99 % Allowed : 24.33 % Favored : 69.68 % 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 aren not related in a simple way. whole: -0.78 (0.27), residues: 1029 helix: 1.14 (0.22), residues: 598 sheet: -1.69 (0.56), residues: 71 loop : -3.27 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.028 0.002 TYR F 38 PHE 0.029 0.002 PHE E 123 TRP 0.021 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8348) covalent geometry : angle 0.75708 (11271) hydrogen bonds : bond 0.03025 ( 435) hydrogen bonds : angle 4.06150 ( 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 356 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.9014 (ttp-170) cc_final: 0.7893 (ttp-170) REVERT: A 37 GLU cc_start: 0.5687 (tt0) cc_final: 0.5076 (tt0) REVERT: A 45 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8026 (p90) REVERT: A 74 ARG cc_start: 0.3482 (tpt-90) cc_final: 0.3091 (tpt-90) REVERT: A 189 ASN cc_start: 0.7107 (m-40) cc_final: 0.6807 (m-40) REVERT: A 248 TYR cc_start: 0.8340 (t80) cc_final: 0.8002 (t80) REVERT: A 321 GLU cc_start: 0.8242 (tp30) cc_final: 0.8007 (tp30) REVERT: B 30 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 40 MET cc_start: 0.8491 (tpp) cc_final: 0.7341 (mtt) REVERT: B 47 ASP cc_start: 0.8320 (p0) cc_final: 0.8082 (p0) REVERT: B 76 SER cc_start: 0.9316 (t) cc_final: 0.9098 (m) REVERT: B 145 ASN cc_start: 0.7640 (p0) cc_final: 0.5779 (m110) REVERT: B 149 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7164 (tm) REVERT: D 19 ASP cc_start: 0.7748 (p0) cc_final: 0.7496 (p0) REVERT: D 25 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7459 (mpp-170) REVERT: D 122 LEU cc_start: 0.9052 (pp) cc_final: 0.8697 (mp) REVERT: E 41 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.6953 (t0) REVERT: E 78 ASP cc_start: 0.8521 (m-30) cc_final: 0.8132 (t0) REVERT: F 27 ARG cc_start: 0.8204 (ptp90) cc_final: 0.7564 (tpt-90) REVERT: F 41 ASN cc_start: 0.8804 (m110) cc_final: 0.8537 (m110) REVERT: F 43 LYS cc_start: 0.5752 (mptt) cc_final: 0.5536 (mptt) REVERT: F 54 LYS cc_start: 0.6864 (tmmt) cc_final: 0.6295 (mttt) REVERT: F 57 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 87 GLN cc_start: 0.8430 (tp-100) cc_final: 0.7962 (tp-100) REVERT: F 91 LEU cc_start: 0.7710 (pp) cc_final: 0.6799 (pp) REVERT: F 143 LYS cc_start: 0.5769 (mppt) cc_final: 0.3594 (mmtt) outliers start: 49 outliers final: 37 residues processed: 330 average time/residue: 0.0992 time to fit residues: 44.6119 Evaluate side-chains 324 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 137 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE 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 231 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 274 THR Chi-restraints excluded: chain A residue 324 ASP 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 149 LEU 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 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain E residue 18 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 91 LEU Chi-restraints excluded: chain E residue 141 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3899 r_free = 0.3899 target = 0.155600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132668 restraints weight = 19239.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134903 restraints weight = 9547.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136204 restraints weight = 5721.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137090 restraints weight = 4026.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137417 restraints weight = 3147.645| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8348 Z= 0.140 Angle : 0.767 10.024 11271 Z= 0.387 Chirality : 0.047 0.200 1255 Planarity : 0.004 0.043 1460 Dihedral : 5.194 33.779 1136 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.23 % Allowed : 25.79 % Favored : 67.97 % 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 aren not related in a simple way. whole: -0.65 (0.27), residues: 1029 helix: 1.25 (0.22), residues: 599 sheet: -1.64 (0.57), residues: 71 loop : -3.24 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 15 TYR 0.021 0.001 TYR D 66 PHE 0.025 0.002 PHE F 109 TRP 0.018 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8348) covalent geometry : angle 0.76654 (11271) hydrogen bonds : bond 0.03055 ( 435) hydrogen bonds : angle 4.14450 ( 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 344 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.4896 (tt0) cc_final: 0.3934 (tt0) REVERT: A 74 ARG cc_start: 0.3504 (tpt-90) cc_final: 0.3168 (tpt-90) REVERT: A 248 TYR cc_start: 0.8375 (t80) cc_final: 0.8065 (t80) REVERT: A 321 GLU cc_start: 0.8310 (tp30) cc_final: 0.8043 (tp30) REVERT: B 30 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 188 ASP cc_start: 0.8519 (p0) cc_final: 0.8196 (m-30) REVERT: B 244 LYS cc_start: 0.7430 (mptt) cc_final: 0.7156 (mmtt) REVERT: D 25 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7442 (mpp-170) REVERT: D 122 LEU cc_start: 0.9038 (pp) cc_final: 0.8586 (mp) REVERT: E 78 ASP cc_start: 0.8494 (m-30) cc_final: 0.8131 (t0) REVERT: E 145 ILE cc_start: 0.7256 (pt) cc_final: 0.6881 (mm) REVERT: F 27 ARG cc_start: 0.8303 (ptp90) cc_final: 0.7569 (tpt-90) REVERT: F 54 LYS cc_start: 0.6901 (tmmt) cc_final: 0.6177 (mttt) REVERT: F 57 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 87 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7942 (tp-100) REVERT: F 91 LEU cc_start: 0.7839 (pp) cc_final: 0.6908 (pp) REVERT: F 131 MET cc_start: 0.7724 (mmp) cc_final: 0.7343 (mmm) outliers start: 51 outliers final: 39 residues processed: 315 average time/residue: 0.0872 time to fit residues: 38.1553 Evaluate side-chains 311 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 231 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 274 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 21 ILE 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 18 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 91 LEU 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 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: 3.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.0770 chunk 90 optimal weight: 0.0980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3930 r_free = 0.3930 target = 0.157995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135521 restraints weight = 19189.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137755 restraints weight = 9430.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139117 restraints weight = 5679.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139974 restraints weight = 3982.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140540 restraints weight = 3126.502| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8348 Z= 0.131 Angle : 0.768 10.085 11271 Z= 0.384 Chirality : 0.046 0.189 1255 Planarity : 0.004 0.045 1460 Dihedral : 5.021 31.463 1136 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.77 % Allowed : 27.75 % Favored : 67.48 % 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 aren not related in a simple way. whole: -0.52 (0.27), residues: 1029 helix: 1.32 (0.22), residues: 600 sheet: -1.33 (0.55), residues: 81 loop : -3.24 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 15 TYR 0.025 0.001 TYR D 66 PHE 0.028 0.002 PHE F 109 TRP 0.015 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8348) covalent geometry : angle 0.76760 (11271) hydrogen bonds : bond 0.02947 ( 435) hydrogen bonds : angle 4.09777 ( 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 323 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.4808 (tt0) cc_final: 0.3725 (tt0) REVERT: A 45 TYR cc_start: 0.8742 (p90) cc_final: 0.7837 (p90) REVERT: A 74 ARG cc_start: 0.3456 (tpt-90) cc_final: 0.3146 (tpt-90) REVERT: A 248 TYR cc_start: 0.8380 (t80) cc_final: 0.8033 (t80) REVERT: A 321 GLU cc_start: 0.8264 (tp30) cc_final: 0.7988 (tp30) REVERT: B 30 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 40 MET cc_start: 0.8375 (tpp) cc_final: 0.7363 (mtt) REVERT: B 244 LYS cc_start: 0.7388 (mptt) cc_final: 0.7074 (mmtt) REVERT: D 25 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7455 (mpp-170) REVERT: D 122 LEU cc_start: 0.9004 (pp) cc_final: 0.8557 (mp) REVERT: E 41 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.6967 (t0) REVERT: E 46 TYR cc_start: 0.8994 (t80) cc_final: 0.8779 (t80) REVERT: E 78 ASP cc_start: 0.8451 (m-30) cc_final: 0.8081 (t0) REVERT: E 145 ILE cc_start: 0.7234 (pt) cc_final: 0.6801 (mm) REVERT: F 27 ARG cc_start: 0.8286 (ptp90) cc_final: 0.7529 (tpt-90) REVERT: F 54 LYS cc_start: 0.6806 (tmmt) cc_final: 0.6118 (mttt) REVERT: F 57 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 87 GLN cc_start: 0.8384 (tp-100) cc_final: 0.7899 (tp-100) REVERT: F 91 LEU cc_start: 0.7820 (pp) cc_final: 0.6883 (pp) REVERT: F 131 MET cc_start: 0.7709 (mmp) cc_final: 0.7372 (mmp) outliers start: 39 outliers final: 30 residues processed: 298 average time/residue: 0.0930 time to fit residues: 38.0017 Evaluate side-chains 311 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 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 324 ASP 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 192 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 18 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 149 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129526 restraints weight = 19144.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131709 restraints weight = 9562.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133020 restraints weight = 5797.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133873 restraints weight = 4116.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134412 restraints weight = 3258.460| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8348 Z= 0.168 Angle : 0.821 11.928 11271 Z= 0.415 Chirality : 0.049 0.228 1255 Planarity : 0.004 0.046 1460 Dihedral : 5.338 35.454 1136 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.75 % Allowed : 28.12 % Favored : 66.14 % 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 aren not related in a simple way. whole: -0.63 (0.27), residues: 1029 helix: 1.21 (0.22), residues: 599 sheet: -1.28 (0.59), residues: 71 loop : -3.22 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 15 TYR 0.026 0.002 TYR D 66 PHE 0.029 0.002 PHE F 109 TRP 0.015 0.002 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8348) covalent geometry : angle 0.82059 (11271) hydrogen bonds : bond 0.03357 ( 435) hydrogen bonds : angle 4.32577 ( 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 327 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8725 (p90) cc_final: 0.7809 (p90) REVERT: A 74 ARG cc_start: 0.3843 (tpt-90) cc_final: 0.3489 (tpt-90) REVERT: A 77 GLN cc_start: 0.9100 (mp10) cc_final: 0.8800 (mp10) REVERT: A 248 TYR cc_start: 0.8541 (t80) cc_final: 0.8224 (t80) REVERT: A 283 LYS cc_start: 0.6356 (mtmt) cc_final: 0.5956 (mtmt) REVERT: A 321 GLU cc_start: 0.8339 (tp30) cc_final: 0.7134 (tp30) REVERT: B 23 GLU cc_start: 0.8019 (pm20) cc_final: 0.7001 (pt0) REVERT: B 30 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8343 (mm) REVERT: B 40 MET cc_start: 0.8315 (tpp) cc_final: 0.7192 (mtt) REVERT: B 145 ASN cc_start: 0.7745 (p0) cc_final: 0.7399 (p0) REVERT: B 244 LYS cc_start: 0.7467 (mptt) cc_final: 0.7135 (mmtt) REVERT: D 25 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7463 (mpp-170) REVERT: D 122 LEU cc_start: 0.8989 (pp) cc_final: 0.8561 (mp) REVERT: D 128 MET cc_start: 0.8025 (mpp) cc_final: 0.6789 (ttm) REVERT: E 46 TYR cc_start: 0.9159 (t80) cc_final: 0.8917 (t80) REVERT: E 145 ILE cc_start: 0.7249 (pt) cc_final: 0.6887 (mm) REVERT: F 27 ARG cc_start: 0.8398 (ptp90) cc_final: 0.7514 (tpt-90) REVERT: F 40 THR cc_start: 0.8448 (p) cc_final: 0.8159 (p) REVERT: F 54 LYS cc_start: 0.6646 (tmmt) cc_final: 0.5998 (mttt) REVERT: F 57 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 67 ASP cc_start: 0.8350 (m-30) cc_final: 0.8150 (m-30) REVERT: F 87 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7867 (tp-100) REVERT: F 91 LEU cc_start: 0.7880 (pp) cc_final: 0.6973 (pp) outliers start: 47 outliers final: 37 residues processed: 298 average time/residue: 0.0910 time to fit residues: 37.5896 Evaluate side-chains 313 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 231 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 274 THR Chi-restraints excluded: chain A residue 278 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 192 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 18 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 91 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 123 PHE 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: 0.9990 chunk 3 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3896 r_free = 0.3896 target = 0.155270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132477 restraints weight = 19234.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134668 restraints weight = 9584.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136013 restraints weight = 5799.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136852 restraints weight = 4109.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137313 restraints weight = 3236.907| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8348 Z= 0.143 Angle : 0.815 11.468 11271 Z= 0.408 Chirality : 0.048 0.214 1255 Planarity : 0.004 0.049 1460 Dihedral : 5.193 33.812 1136 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.40 % Allowed : 29.10 % Favored : 66.50 % 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 aren not related in a simple way. whole: -0.46 (0.28), residues: 1029 helix: 1.35 (0.22), residues: 598 sheet: -0.93 (0.61), residues: 71 loop : -3.19 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 15 TYR 0.026 0.001 TYR D 66 PHE 0.025 0.002 PHE F 109 TRP 0.014 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8348) covalent geometry : angle 0.81533 (11271) hydrogen bonds : bond 0.03140 ( 435) hydrogen bonds : angle 4.24160 ( 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 323 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8667 (p90) cc_final: 0.7905 (p90) REVERT: A 74 ARG cc_start: 0.3649 (tpt-90) cc_final: 0.3293 (tpt-90) REVERT: A 77 GLN cc_start: 0.9020 (mp10) cc_final: 0.8725 (mp10) REVERT: A 248 TYR cc_start: 0.8456 (t80) cc_final: 0.8103 (t80) REVERT: A 283 LYS cc_start: 0.6317 (mtmt) cc_final: 0.5897 (mtmt) REVERT: B 18 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8817 (ttpt) REVERT: B 23 GLU cc_start: 0.7985 (pm20) cc_final: 0.6917 (pt0) REVERT: B 30 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 40 MET cc_start: 0.8090 (tpp) cc_final: 0.7109 (mtt) REVERT: B 145 ASN cc_start: 0.7492 (p0) cc_final: 0.7154 (p0) REVERT: B 188 ASP cc_start: 0.8386 (p0) cc_final: 0.8092 (m-30) REVERT: B 244 LYS cc_start: 0.7455 (mptt) cc_final: 0.7149 (mmtt) REVERT: D 25 ARG cc_start: 0.8096 (ttt180) cc_final: 0.7448 (mpp-170) REVERT: D 122 LEU cc_start: 0.8992 (pp) cc_final: 0.8567 (mp) REVERT: D 128 MET cc_start: 0.7884 (mpp) cc_final: 0.6837 (ttm) REVERT: D 141 LEU cc_start: 0.8600 (pp) cc_final: 0.8229 (mt) REVERT: E 20 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 46 TYR cc_start: 0.9112 (t80) cc_final: 0.8881 (t80) REVERT: E 145 ILE cc_start: 0.7311 (pt) cc_final: 0.6908 (mm) REVERT: F 27 ARG cc_start: 0.8366 (ptp90) cc_final: 0.7509 (tpt-90) REVERT: F 40 THR cc_start: 0.8209 (p) cc_final: 0.7889 (p) REVERT: F 43 LYS cc_start: 0.5748 (mptt) cc_final: 0.5490 (mptt) REVERT: F 54 LYS cc_start: 0.6868 (tmmt) cc_final: 0.6147 (mttt) REVERT: F 57 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8063 (tm-30) REVERT: F 87 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7882 (tp-100) REVERT: F 131 MET cc_start: 0.8040 (mmp) cc_final: 0.7685 (mmm) outliers start: 36 outliers final: 30 residues processed: 301 average time/residue: 0.0910 time to fit residues: 37.7605 Evaluate side-chains 312 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 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 108 THR Chi-restraints excluded: chain A residue 137 SER 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 222 LEU Chi-restraints excluded: chain A residue 231 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 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 192 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 21 ILE 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 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 22 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3863 r_free = 0.3863 target = 0.152880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129657 restraints weight = 19274.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131829 restraints weight = 9658.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133085 restraints weight = 5874.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133972 restraints weight = 4197.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134199 restraints weight = 3310.794| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8348 Z= 0.170 Angle : 0.838 11.089 11271 Z= 0.422 Chirality : 0.049 0.257 1255 Planarity : 0.004 0.049 1460 Dihedral : 5.403 34.545 1136 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.77 % Allowed : 28.73 % Favored : 66.50 % 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 aren not related in a simple way. whole: -0.54 (0.27), residues: 1029 helix: 1.28 (0.22), residues: 599 sheet: -0.94 (0.61), residues: 71 loop : -3.25 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 15 TYR 0.016 0.002 TYR F 112 PHE 0.030 0.002 PHE F 109 TRP 0.015 0.002 TRP F 95 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8348) covalent geometry : angle 0.83815 (11271) hydrogen bonds : bond 0.03375 ( 435) hydrogen bonds : angle 4.35041 ( 1278) =============================================================================== Job complete usr+sys time: 2242.74 seconds wall clock time: 39 minutes 14.71 seconds (2354.71 seconds total)