Starting phenix.real_space_refine on Wed Feb 12 14:27:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iac_4435/02_2025/6iac_4435.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iac_4435/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2025/6iac_4435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2025/6iac_4435.map" model { file = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2025/6iac_4435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2025/6iac_4435.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} 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, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'GLU:plan': 2, '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: {'GLN:plan1': 3, 'GLU:plan': 2, '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: {'GLN:plan1': 6, 'GLU:plan': 2, '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: {'GLN:plan1': 6, 'GLU:plan': 2, '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: {'GLN:plan1': 4, 'GLU:plan': 2, '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: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 5.89, per 1000 atoms: 0.72 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.70 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: 1.94 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2182 1.33 - 1.45: 1673 1.45 - 1.57: 4450 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8348 Sorted by residual: bond pdb=" C ARG D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C GLU A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.523 1.570 -0.046 1.80e-02 3.09e+03 6.65e+00 bond pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.09e+00 bond pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 ... (remaining 8343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 10997 3.58 - 7.16: 225 7.16 - 10.74: 42 10.74 - 14.32: 5 14.32 - 17.90: 2 Bond angle restraints: 11271 Sorted by residual: angle pdb=" C THR A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C LYS D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA TYR A 45 " pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 113.90 123.83 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C ASP A 153 " pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " ideal model delta sigma weight residual 110.36 100.37 9.99 1.85e+00 2.92e-01 2.92e+01 angle pdb=" C ASP A 264 " pdb=" N GLU A 265 " pdb=" CA GLU A 265 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 ... (remaining 11266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4589 16.07 - 32.14: 371 32.14 - 48.21: 78 48.21 - 64.28: 1 64.28 - 80.34: 6 Dihedral angle restraints: 5045 sinusoidal: 1896 harmonic: 3149 Sorted by residual: dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta harmonic sigma weight residual -180.00 -139.12 -40.88 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N SER B 115 " pdb=" CA SER B 115 " ideal model delta harmonic sigma weight residual -180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA TYR B 113 " pdb=" C TYR B 113 " pdb=" N SER B 114 " pdb=" CA SER B 114 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 210 0.158 - 0.237: 40 0.237 - 0.316: 6 0.316 - 0.395: 2 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA TYR A 45 " pdb=" N TYR A 45 " pdb=" C TYR A 45 " pdb=" CB TYR A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1252 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 90 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C ASP D 90 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP D 90 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 91 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 46 " -0.034 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR F 46 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR F 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 46 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 46 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 46 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR F 46 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 46 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 45 " -0.035 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 45 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2080 2.78 - 3.31: 7828 3.31 - 3.84: 12670 3.84 - 4.37: 13537 4.37 - 4.90: 22438 Nonbonded interactions: 58553 Sorted by model distance: nonbonded pdb=" O ILE A 157 " pdb=" OG1 THR A 161 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 292 " pdb=" O LEU A 297 " model vdw 2.261 3.040 nonbonded pdb=" O PHE A 273 " pdb=" OG SER A 276 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR D 66 " pdb=" OD1 ASP F 67 " model vdw 2.314 3.040 nonbonded pdb=" O THR A 108 " pdb=" OH TYR A 132 " model vdw 2.318 3.040 ... (remaining 58548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 144)) selection = (chain 'E' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or r \ esid 52 through 105 or (resid 106 through 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 through 144)) selection = (chain 'F' and (resid 24 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 105 or (resid 106 thr \ ough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 t \ hrough 110 or (resid 111 and (name N or name CA or name C or name O or name CB ) \ ) or resid 112 through 144)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 77 through 98) selection = (chain 'J' and resid 77 through 98) selection = (chain 'K' and (name N or name CA or name C or name O or name CB )) selection = (chain 'L' and resid 77 through 98) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- 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= 0.607 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.004 TRP F 95 HIS 0.021 0.006 HIS E 106 PHE 0.064 0.005 PHE D 31 TYR 0.066 0.005 TYR A 45 ARG 0.014 0.001 ARG A 24 *********************** 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 : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.9033 (mp10) REVERT: A 185 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7669 (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: 0.8346 (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 259 GLU cc_start: 0.7944 (mp0) cc_final: 0.7744 (mp0) REVERT: A 303 TYR cc_start: 0.8185 (t80) cc_final: 0.7853 (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: 0.8796 (ttpt) REVERT: B 47 ASP cc_start: 0.8620 (p0) cc_final: 0.8159 (p0) REVERT: B 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9250 (tp) REVERT: B 125 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7909 (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: 0.8177 (tt) REVERT: D 25 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7589 (mpp-170) 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: 0.7704 (mmpt) REVERT: D 87 GLN cc_start: 0.9137 (mt0) cc_final: 0.8898 (mt0) REVERT: D 89 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7979 (tmtt) REVERT: D 90 ASP cc_start: 0.7751 (t0) cc_final: 0.7397 (p0) REVERT: D 133 ASP cc_start: 0.8682 (t0) cc_final: 0.8155 (t70) REVERT: E 14 ILE cc_start: 0.8274 (mm) cc_final: 0.7959 (pt) REVERT: E 17 PHE cc_start: 0.9141 (m-80) cc_final: 0.8862 (m-10) REVERT: E 22 TYR cc_start: 0.8511 (t80) cc_final: 0.7943 (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: 0.7402 (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: 0.8376 (m-30) REVERT: E 104 ILE cc_start: 0.8808 (mt) cc_final: 0.8007 (mm) REVERT: F 27 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7752 (tpt-90) REVERT: F 43 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8338 (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: 0.8379 (tm-30) REVERT: F 68 ASN cc_start: 0.8697 (t0) cc_final: 0.8439 (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: 0.6732 (t80) REVERT: F 125 VAL cc_start: 0.9406 (t) cc_final: 0.9038 (p) REVERT: F 131 MET cc_start: 0.7930 (mmt) cc_final: 0.7729 (mmm) REVERT: F 143 LYS cc_start: 0.5689 (mppt) cc_final: 0.4091 (mmtt) outliers start: 9 outliers final: 2 residues processed: 420 average time/residue: 0.2350 time to fit residues: 127.9101 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 : 0.935 ------------------------------------------------------------------------------- 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 85 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127496 restraints weight = 18677.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129814 restraints weight = 9384.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131273 restraints weight = 5692.123| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8348 Z= 0.243 Angle : 0.778 12.452 11271 Z= 0.415 Chirality : 0.048 0.230 1255 Planarity : 0.005 0.048 1460 Dihedral : 6.697 35.671 1138 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.01 % Allowed : 16.99 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1029 helix: -0.37 (0.20), residues: 594 sheet: -3.36 (0.47), residues: 69 loop : -3.66 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 95 HIS 0.004 0.001 HIS E 106 PHE 0.027 0.002 PHE F 84 TYR 0.025 0.002 TYR A 45 ARG 0.006 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 45 TYR cc_start: 0.8858 (p90) cc_final: 0.7407 (p90) REVERT: A 55 PHE cc_start: 0.8695 (m-80) cc_final: 0.8441 (m-80) REVERT: A 57 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 74 ARG cc_start: 0.6890 (mmp-170) cc_final: 0.6612 (tpt-90) REVERT: A 76 LYS cc_start: 0.8631 (pttt) cc_final: 0.8068 (ptmt) REVERT: A 77 GLN cc_start: 0.9214 (mp10) cc_final: 0.8718 (mp10) REVERT: A 160 TYR cc_start: 0.8736 (m-80) cc_final: 0.8408 (m-80) REVERT: A 163 GLU cc_start: 0.7876 (tt0) cc_final: 0.7583 (tt0) REVERT: A 185 LYS cc_start: 0.7178 (ttmt) cc_final: 0.6580 (tmtt) REVERT: A 248 TYR cc_start: 0.8502 (t80) cc_final: 0.8223 (t80) REVERT: A 251 ILE cc_start: 0.9324 (pp) cc_final: 0.8901 (pp) REVERT: A 303 TYR cc_start: 0.7886 (t80) cc_final: 0.7486 (t80) REVERT: B 38 GLN cc_start: 0.7885 (pm20) cc_final: 0.7371 (pt0) REVERT: B 229 ASP cc_start: 0.7803 (t0) cc_final: 0.7569 (t0) REVERT: B 245 LYS cc_start: 0.8382 (mttt) cc_final: 0.8127 (mttt) REVERT: D 25 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7428 (mpp-170) REVERT: D 96 LEU cc_start: 0.7190 (pp) cc_final: 0.5912 (pp) REVERT: D 122 LEU cc_start: 0.9086 (pp) cc_final: 0.8661 (mp) REVERT: D 141 LEU cc_start: 0.8848 (mt) cc_final: 0.8553 (pp) REVERT: E 17 PHE cc_start: 0.9036 (m-80) cc_final: 0.8827 (m-10) REVERT: E 22 TYR cc_start: 0.8490 (t80) cc_final: 0.7926 (t80) REVERT: E 46 TYR cc_start: 0.9204 (t80) cc_final: 0.8667 (t80) REVERT: E 78 ASP cc_start: 0.8546 (m-30) cc_final: 0.8000 (t0) REVERT: E 86 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 27 ARG cc_start: 0.8222 (ptp90) cc_final: 0.7634 (tpt-90) REVERT: F 43 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8338 (mptt) REVERT: F 54 LYS cc_start: 0.6903 (tmmt) cc_final: 0.6259 (mttt) REVERT: F 57 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8122 (tm-30) REVERT: F 78 ASP cc_start: 0.7945 (m-30) cc_final: 0.7595 (m-30) REVERT: F 87 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8047 (tp-100) REVERT: F 91 LEU cc_start: 0.7600 (pp) cc_final: 0.6614 (pp) REVERT: F 116 LEU cc_start: 0.9168 (mt) cc_final: 0.8907 (mt) REVERT: F 143 LYS cc_start: 0.5670 (mppt) cc_final: 0.3675 (mmtt) outliers start: 41 outliers final: 24 residues processed: 371 average time/residue: 0.2182 time to fit residues: 106.4287 Evaluate side-chains 334 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 309 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 196 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 97 ASN 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 26 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.149025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125138 restraints weight = 19015.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127256 restraints weight = 9733.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128610 restraints weight = 5995.669| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8348 Z= 0.285 Angle : 0.783 9.508 11271 Z= 0.414 Chirality : 0.049 0.204 1255 Planarity : 0.004 0.040 1460 Dihedral : 6.243 37.648 1136 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 6.60 % Allowed : 19.80 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.26), residues: 1029 helix: 0.38 (0.22), residues: 597 sheet: -3.23 (0.50), residues: 69 loop : -3.62 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 95 HIS 0.011 0.002 HIS B 130 PHE 0.027 0.003 PHE D 109 TYR 0.024 0.002 TYR E 45 ARG 0.007 0.001 ARG A 285 *********************** 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 370 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2704 (ptt-90) cc_final: 0.2268 (ptt-90) REVERT: A 37 GLU cc_start: 0.6407 (tt0) cc_final: 0.5861 (tt0) REVERT: A 39 LEU cc_start: 0.9623 (tt) cc_final: 0.9412 (tp) REVERT: A 45 TYR cc_start: 0.8846 (p90) cc_final: 0.8598 (p90) REVERT: A 57 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 74 ARG cc_start: 0.6820 (mmp-170) cc_final: 0.6619 (tpt-90) REVERT: A 76 LYS cc_start: 0.8684 (pttt) cc_final: 0.7902 (ptmt) REVERT: A 77 GLN cc_start: 0.9236 (mp10) cc_final: 0.8721 (mp10) REVERT: A 241 LYS cc_start: 0.9173 (tppp) cc_final: 0.8737 (tppp) REVERT: B 23 GLU cc_start: 0.8278 (pm20) cc_final: 0.7290 (pt0) REVERT: B 30 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 47 ASP cc_start: 0.8640 (p0) cc_final: 0.8326 (p0) REVERT: B 245 LYS cc_start: 0.8301 (mttt) cc_final: 0.8035 (mttt) REVERT: D 25 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7374 (mpp-170) REVERT: D 122 LEU cc_start: 0.9097 (pp) cc_final: 0.8690 (mp) REVERT: D 141 LEU cc_start: 0.8864 (mt) cc_final: 0.8652 (pp) REVERT: F 27 ARG cc_start: 0.8177 (ptp90) cc_final: 0.7562 (tpt-90) REVERT: F 43 LYS cc_start: 0.8638 (mtpm) cc_final: 0.8431 (mptt) REVERT: F 54 LYS cc_start: 0.7031 (tmmt) cc_final: 0.6353 (mttm) REVERT: F 57 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 78 ASP cc_start: 0.7919 (m-30) cc_final: 0.7643 (m-30) REVERT: F 87 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8071 (tp-100) REVERT: F 91 LEU cc_start: 0.7661 (pp) cc_final: 0.6791 (pp) REVERT: F 131 MET cc_start: 0.7880 (mmp) cc_final: 0.7601 (mmp) outliers start: 54 outliers final: 34 residues processed: 338 average time/residue: 0.2041 time to fit residues: 92.7176 Evaluate side-chains 330 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 68 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 ASP 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 D residue 91 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 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 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129313 restraints weight = 18982.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131527 restraints weight = 9488.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132929 restraints weight = 5834.637| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8348 Z= 0.182 Angle : 0.748 11.809 11271 Z= 0.381 Chirality : 0.046 0.192 1255 Planarity : 0.004 0.034 1460 Dihedral : 5.716 35.205 1136 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.99 % Allowed : 21.88 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 1029 helix: 0.77 (0.22), residues: 596 sheet: -2.50 (0.55), residues: 71 loop : -3.45 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.016 0.002 PHE A 55 TYR 0.022 0.002 TYR F 112 ARG 0.005 0.000 ARG A 285 *********************** 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 366 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2500 (ptt-90) cc_final: 0.2146 (ptt-90) REVERT: A 37 GLU cc_start: 0.6148 (tt0) cc_final: 0.5729 (tt0) REVERT: A 45 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8333 (p90) REVERT: A 57 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 74 ARG cc_start: 0.6801 (mmp-170) cc_final: 0.6564 (tpt-90) REVERT: A 77 GLN cc_start: 0.9144 (mp10) cc_final: 0.8679 (mp10) REVERT: A 241 LYS cc_start: 0.9072 (tppp) cc_final: 0.8791 (tppp) REVERT: A 242 ILE cc_start: 0.9154 (tt) cc_final: 0.8861 (tt) REVERT: A 248 TYR cc_start: 0.8416 (t80) cc_final: 0.8143 (t80) REVERT: B 30 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 40 MET cc_start: 0.8747 (tpp) cc_final: 0.7379 (mtt) REVERT: D 25 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7371 (mpp-170) REVERT: D 87 GLN cc_start: 0.8869 (mt0) cc_final: 0.8643 (mp10) REVERT: D 93 ARG cc_start: 0.7622 (mmp80) cc_final: 0.7265 (mmp80) REVERT: D 122 LEU cc_start: 0.9037 (pp) cc_final: 0.8623 (mp) REVERT: E 50 SER cc_start: 0.9125 (t) cc_final: 0.8866 (t) REVERT: E 52 LEU cc_start: 0.9198 (tp) cc_final: 0.8913 (tt) REVERT: E 78 ASP cc_start: 0.8545 (m-30) cc_final: 0.8059 (t0) REVERT: E 120 PHE cc_start: 0.6555 (m-10) cc_final: 0.6186 (m-10) REVERT: E 145 ILE cc_start: 0.7199 (pt) cc_final: 0.6913 (mm) REVERT: F 27 ARG cc_start: 0.8152 (ptp90) cc_final: 0.7545 (tpt-90) REVERT: F 54 LYS cc_start: 0.6933 (tmmt) cc_final: 0.6266 (mttm) REVERT: F 57 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8084 (tm-30) REVERT: F 78 ASP cc_start: 0.7767 (m-30) cc_final: 0.7545 (m-30) REVERT: F 87 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7989 (tp-100) REVERT: F 91 LEU cc_start: 0.7631 (pp) cc_final: 0.6685 (pp) REVERT: F 128 MET cc_start: 0.8649 (mmm) cc_final: 0.8410 (mmm) REVERT: F 131 MET cc_start: 0.7912 (mmp) cc_final: 0.7490 (mmp) outliers start: 49 outliers final: 37 residues processed: 335 average time/residue: 0.2007 time to fit residues: 90.7196 Evaluate side-chains 330 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 68 VAL Chi-restraints excluded: chain A residue 69 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 222 LEU Chi-restraints excluded: chain A residue 243 SER 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 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 21 ILE 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 18 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 145 ASN B 189 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130524 restraints weight = 18870.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132752 restraints weight = 9300.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134084 restraints weight = 5585.186| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8348 Z= 0.178 Angle : 0.736 9.262 11271 Z= 0.378 Chirality : 0.046 0.217 1255 Planarity : 0.004 0.035 1460 Dihedral : 5.438 34.912 1136 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.11 % Allowed : 23.59 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 1029 helix: 0.92 (0.22), residues: 599 sheet: -2.22 (0.56), residues: 71 loop : -3.35 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 PHE 0.045 0.002 PHE D 109 TYR 0.018 0.001 TYR F 112 ARG 0.004 0.000 ARG A 285 *********************** 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 360 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5415 (tt0) cc_final: 0.5013 (tt0) REVERT: A 45 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7899 (p90) REVERT: A 57 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 74 ARG cc_start: 0.6754 (mmp-170) cc_final: 0.6514 (tpt-90) REVERT: A 77 GLN cc_start: 0.9154 (mp10) cc_final: 0.8687 (mp10) REVERT: A 241 LYS cc_start: 0.9014 (tppp) cc_final: 0.8657 (tppt) REVERT: A 242 ILE cc_start: 0.9101 (tt) cc_final: 0.8830 (tt) REVERT: B 30 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8351 (mm) REVERT: B 40 MET cc_start: 0.8730 (tpp) cc_final: 0.7309 (mtt) REVERT: B 76 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.9053 (m) REVERT: B 188 ASP cc_start: 0.8465 (p0) cc_final: 0.8224 (m-30) REVERT: B 245 LYS cc_start: 0.8234 (mttt) cc_final: 0.7960 (mttt) REVERT: D 25 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7360 (mpp-170) REVERT: D 38 TYR cc_start: 0.8790 (m-80) cc_final: 0.8537 (m-80) REVERT: D 87 GLN cc_start: 0.8811 (mt0) cc_final: 0.8541 (mp10) REVERT: D 122 LEU cc_start: 0.9067 (pp) cc_final: 0.8642 (mp) REVERT: D 123 PHE cc_start: 0.9050 (t80) cc_final: 0.8741 (t80) REVERT: E 52 LEU cc_start: 0.9161 (tp) cc_final: 0.8915 (tt) REVERT: E 78 ASP cc_start: 0.8513 (m-30) cc_final: 0.8024 (t0) REVERT: E 145 ILE cc_start: 0.7131 (pt) cc_final: 0.6866 (mm) REVERT: F 27 ARG cc_start: 0.8264 (ptp90) cc_final: 0.7552 (tpt-90) REVERT: F 54 LYS cc_start: 0.6927 (tmmt) cc_final: 0.6261 (mttt) REVERT: F 57 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 78 ASP cc_start: 0.7869 (m-30) cc_final: 0.7606 (m-30) REVERT: F 87 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7965 (tp-100) REVERT: F 91 LEU cc_start: 0.7678 (pp) cc_final: 0.6730 (pp) REVERT: F 128 MET cc_start: 0.8575 (mmm) cc_final: 0.8336 (mmm) outliers start: 50 outliers final: 40 residues processed: 330 average time/residue: 0.2041 time to fit residues: 90.6123 Evaluate side-chains 331 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 21 ILE 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 120 PHE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 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 95 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 65 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127209 restraints weight = 19027.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129377 restraints weight = 9497.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130736 restraints weight = 5776.462| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8348 Z= 0.238 Angle : 0.770 9.437 11271 Z= 0.395 Chirality : 0.048 0.241 1255 Planarity : 0.004 0.039 1460 Dihedral : 5.578 37.854 1136 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 7.09 % Allowed : 23.84 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 1029 helix: 1.02 (0.22), residues: 599 sheet: -2.21 (0.53), residues: 81 loop : -3.36 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 95 HIS 0.003 0.001 HIS B 105 PHE 0.023 0.002 PHE F 134 TYR 0.029 0.002 TYR E 45 ARG 0.007 0.001 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5249 (tt0) cc_final: 0.4483 (tt0) REVERT: A 45 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8110 (p90) REVERT: A 57 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 74 ARG cc_start: 0.6692 (mmp-170) cc_final: 0.6473 (tpt170) REVERT: A 77 GLN cc_start: 0.9174 (mp10) cc_final: 0.8653 (mp10) REVERT: A 241 LYS cc_start: 0.9014 (tppp) cc_final: 0.8753 (tppt) REVERT: A 242 ILE cc_start: 0.9249 (tt) cc_final: 0.9014 (tt) REVERT: B 30 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 40 MET cc_start: 0.8698 (tpp) cc_final: 0.7332 (mtt) REVERT: B 76 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9052 (m) REVERT: B 188 ASP cc_start: 0.8599 (p0) cc_final: 0.8207 (m-30) REVERT: B 243 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8701 (t0) REVERT: B 244 LYS cc_start: 0.7438 (mptt) cc_final: 0.7110 (mmtt) REVERT: D 25 ARG cc_start: 0.8112 (ttt180) cc_final: 0.7392 (mpp-170) REVERT: D 67 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: D 87 GLN cc_start: 0.8832 (mt0) cc_final: 0.8559 (mp10) REVERT: D 122 LEU cc_start: 0.9074 (pp) cc_final: 0.8632 (mp) REVERT: D 123 PHE cc_start: 0.9078 (t80) cc_final: 0.8827 (t80) REVERT: E 46 TYR cc_start: 0.9291 (t80) cc_final: 0.8951 (t80) REVERT: E 52 LEU cc_start: 0.9187 (tp) cc_final: 0.8906 (tt) REVERT: F 27 ARG cc_start: 0.8353 (ptp90) cc_final: 0.7557 (tpt-90) REVERT: F 45 TYR cc_start: 0.8224 (m-80) cc_final: 0.8015 (m-80) REVERT: F 54 LYS cc_start: 0.7003 (tmmt) cc_final: 0.6345 (mttt) REVERT: F 57 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8142 (tm-30) REVERT: F 87 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7963 (tp-100) outliers start: 58 outliers final: 45 residues processed: 326 average time/residue: 0.2035 time to fit residues: 89.2132 Evaluate side-chains 344 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain D residue 21 ILE 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 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 74 PHE 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 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 68 ASN 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 32 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 145 ASN F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126930 restraints weight = 18963.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129032 restraints weight = 9540.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130371 restraints weight = 5832.164| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8348 Z= 0.255 Angle : 0.795 9.137 11271 Z= 0.407 Chirality : 0.049 0.204 1255 Planarity : 0.004 0.044 1460 Dihedral : 5.642 37.979 1136 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 7.33 % Allowed : 26.04 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 1029 helix: 1.06 (0.22), residues: 596 sheet: -2.16 (0.54), residues: 81 loop : -3.43 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 95 HIS 0.003 0.001 HIS B 105 PHE 0.043 0.002 PHE D 109 TYR 0.022 0.002 TYR A 160 ARG 0.008 0.001 ARG D 15 *********************** 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 362 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.4938 (tt0) cc_final: 0.3921 (tt0) REVERT: A 45 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8179 (p90) REVERT: A 57 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 74 ARG cc_start: 0.6749 (mmp-170) cc_final: 0.6533 (tpt170) REVERT: A 77 GLN cc_start: 0.9115 (mp10) cc_final: 0.8794 (mp10) REVERT: A 166 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6370 (pp20) REVERT: A 321 GLU cc_start: 0.8435 (tp30) cc_final: 0.7355 (tp30) REVERT: B 18 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8908 (ttpt) REVERT: B 40 MET cc_start: 0.8743 (tpp) cc_final: 0.7505 (mtm) REVERT: B 76 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.9059 (m) REVERT: B 123 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 244 LYS cc_start: 0.7469 (mptt) cc_final: 0.6956 (tppt) REVERT: D 25 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7401 (mpp-170) REVERT: D 67 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: D 75 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7827 (mmpt) REVERT: D 87 GLN cc_start: 0.8835 (mt0) cc_final: 0.8546 (mp10) REVERT: D 122 LEU cc_start: 0.9065 (pp) cc_final: 0.8621 (mp) REVERT: E 46 TYR cc_start: 0.9183 (t80) cc_final: 0.8919 (t80) REVERT: E 52 LEU cc_start: 0.9188 (tp) cc_final: 0.8932 (tt) REVERT: E 69 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8486 (tm-30) REVERT: E 145 ILE cc_start: 0.7260 (pt) cc_final: 0.6899 (mm) REVERT: F 27 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7654 (tpt-90) REVERT: F 51 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.8330 (ttm-80) REVERT: F 54 LYS cc_start: 0.7001 (tmmt) cc_final: 0.6334 (mttt) REVERT: F 57 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8121 (tm-30) REVERT: F 87 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7756 (tp-100) REVERT: F 128 MET cc_start: 0.8420 (mmm) cc_final: 0.8194 (mmm) outliers start: 60 outliers final: 44 residues processed: 326 average time/residue: 0.1966 time to fit residues: 86.2219 Evaluate side-chains 343 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain D residue 21 ILE 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 42 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.155257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132627 restraints weight = 18991.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134830 restraints weight = 9204.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136224 restraints weight = 5452.920| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8348 Z= 0.184 Angle : 0.767 10.207 11271 Z= 0.389 Chirality : 0.047 0.228 1255 Planarity : 0.004 0.044 1460 Dihedral : 5.248 34.288 1136 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.62 % Allowed : 27.26 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 1029 helix: 1.20 (0.22), residues: 600 sheet: -1.85 (0.54), residues: 81 loop : -3.33 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 77 HIS 0.003 0.001 HIS A 159 PHE 0.016 0.002 PHE A 55 TYR 0.027 0.001 TYR E 112 ARG 0.011 0.001 ARG D 15 *********************** 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 366 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.4982 (tt0) cc_final: 0.4062 (tt0) REVERT: A 45 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8159 (p90) REVERT: A 58 LEU cc_start: 0.9269 (tt) cc_final: 0.8960 (tp) REVERT: A 74 ARG cc_start: 0.6770 (mmp-170) cc_final: 0.6533 (tpt170) REVERT: A 77 GLN cc_start: 0.9007 (mp10) cc_final: 0.8549 (mp10) REVERT: A 155 GLU cc_start: 0.8124 (tp30) cc_final: 0.7715 (tp30) REVERT: B 18 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8909 (tttt) REVERT: B 23 GLU cc_start: 0.7920 (pm20) cc_final: 0.6956 (pt0) REVERT: B 40 MET cc_start: 0.8626 (tpp) cc_final: 0.7474 (mtt) REVERT: B 76 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.9058 (m) REVERT: B 88 ARG cc_start: 0.6395 (mmt180) cc_final: 0.5826 (mmm160) REVERT: B 199 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: B 244 LYS cc_start: 0.7358 (mptt) cc_final: 0.7102 (mmtt) REVERT: D 25 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7395 (mpp-170) REVERT: D 53 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.8655 (t) REVERT: D 67 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: D 69 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7136 (tm-30) REVERT: D 87 GLN cc_start: 0.8825 (mt0) cc_final: 0.8514 (mp10) REVERT: D 122 LEU cc_start: 0.9069 (pp) cc_final: 0.8566 (mp) REVERT: E 20 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 46 TYR cc_start: 0.9027 (t80) cc_final: 0.8801 (t80) REVERT: E 69 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8516 (tm-30) REVERT: E 145 ILE cc_start: 0.7279 (pt) cc_final: 0.6914 (mm) REVERT: F 27 ARG cc_start: 0.8451 (ptp90) cc_final: 0.7650 (tpt-90) REVERT: F 54 LYS cc_start: 0.6878 (tmmt) cc_final: 0.6313 (mttt) REVERT: F 57 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8054 (tm-30) REVERT: F 87 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7673 (tp-100) REVERT: F 131 MET cc_start: 0.7651 (mmm) cc_final: 0.7414 (mmm) outliers start: 46 outliers final: 32 residues processed: 336 average time/residue: 0.2084 time to fit residues: 94.1308 Evaluate side-chains 332 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 76 SER 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 B residue 223 TYR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 PHE 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 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 80 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 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.155350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132708 restraints weight = 19301.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134959 restraints weight = 9416.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136320 restraints weight = 5568.746| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5984 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= 0.197 Angle : 0.808 10.772 11271 Z= 0.401 Chirality : 0.047 0.204 1255 Planarity : 0.004 0.050 1460 Dihedral : 5.129 33.639 1136 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.62 % Allowed : 28.85 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.28), residues: 1029 helix: 1.22 (0.23), residues: 597 sheet: -1.67 (0.54), residues: 83 loop : -3.31 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 PHE 0.045 0.002 PHE D 109 TYR 0.018 0.001 TYR F 112 ARG 0.011 0.001 ARG D 15 *********************** 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 357 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.4978 (tt0) cc_final: 0.3737 (tt0) REVERT: A 45 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8073 (p90) REVERT: A 77 GLN cc_start: 0.9019 (mp10) cc_final: 0.8701 (mp10) REVERT: A 283 LYS cc_start: 0.6251 (mtmt) cc_final: 0.5948 (mtmt) REVERT: B 40 MET cc_start: 0.8678 (tpp) cc_final: 0.7375 (mtt) REVERT: B 76 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.9086 (m) REVERT: B 88 ARG cc_start: 0.6365 (mmt180) cc_final: 0.5844 (mmm160) REVERT: B 188 ASP cc_start: 0.8507 (p0) cc_final: 0.8250 (m-30) REVERT: B 244 LYS cc_start: 0.7428 (mptt) cc_final: 0.7110 (mmtt) REVERT: D 25 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7395 (mpp-170) REVERT: D 53 SER cc_start: 0.9056 (m) cc_final: 0.8724 (t) REVERT: D 87 GLN cc_start: 0.8772 (mt0) cc_final: 0.8438 (mp10) REVERT: D 122 LEU cc_start: 0.9021 (pp) cc_final: 0.8505 (mp) REVERT: E 20 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 46 TYR cc_start: 0.9032 (t80) cc_final: 0.8809 (t80) REVERT: E 145 ILE cc_start: 0.7319 (pt) cc_final: 0.6944 (mm) REVERT: F 27 ARG cc_start: 0.8430 (ptp90) cc_final: 0.7581 (tpt-90) REVERT: F 54 LYS cc_start: 0.6911 (tmmt) cc_final: 0.6320 (mttt) REVERT: F 57 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8039 (tm-30) REVERT: F 87 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7793 (tp-100) outliers start: 46 outliers final: 35 residues processed: 326 average time/residue: 0.2118 time to fit residues: 92.6156 Evaluate side-chains 336 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 ARG 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 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 0.0270 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 16 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135081 restraints weight = 18977.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137289 restraints weight = 9292.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138631 restraints weight = 5542.134| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.6275 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= 0.207 Angle : 0.855 12.813 11271 Z= 0.423 Chirality : 0.047 0.231 1255 Planarity : 0.004 0.050 1460 Dihedral : 4.970 31.820 1136 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.65 % Allowed : 30.32 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 1029 helix: 1.28 (0.22), residues: 598 sheet: -1.25 (0.56), residues: 83 loop : -3.34 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 95 HIS 0.003 0.001 HIS A 159 PHE 0.040 0.001 PHE D 109 TYR 0.018 0.001 TYR E 112 ARG 0.012 0.001 ARG D 15 ********************** 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 344 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.5008 (tt0) cc_final: 0.3653 (tt0) REVERT: A 77 GLN cc_start: 0.8999 (mp10) cc_final: 0.8646 (mp10) REVERT: A 160 TYR cc_start: 0.7922 (m-80) cc_final: 0.7649 (m-80) REVERT: A 244 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 283 LYS cc_start: 0.6176 (mtmt) cc_final: 0.5855 (mtmt) REVERT: B 23 GLU cc_start: 0.7928 (pm20) cc_final: 0.6955 (pt0) REVERT: B 40 MET cc_start: 0.8618 (tpp) cc_final: 0.7275 (mtt) REVERT: B 76 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9073 (m) REVERT: B 88 ARG cc_start: 0.6515 (mmt180) cc_final: 0.6095 (mmm160) REVERT: D 25 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7435 (mpp-170) REVERT: D 81 MET cc_start: 0.8691 (mmm) cc_final: 0.8486 (mmm) REVERT: D 87 GLN cc_start: 0.8729 (mt0) cc_final: 0.8404 (mp10) REVERT: D 109 PHE cc_start: 0.6229 (m-80) cc_final: 0.5437 (m-80) REVERT: D 122 LEU cc_start: 0.9028 (pp) cc_final: 0.8540 (mp) REVERT: E 46 TYR cc_start: 0.8969 (t80) cc_final: 0.8729 (t80) REVERT: E 145 ILE cc_start: 0.6989 (pt) cc_final: 0.6648 (mm) REVERT: F 27 ARG cc_start: 0.8401 (ptp90) cc_final: 0.7544 (tpt-90) REVERT: F 54 LYS cc_start: 0.6898 (tmmt) cc_final: 0.6307 (mttt) REVERT: F 57 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7973 (tm-30) REVERT: F 87 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7765 (tp-100) outliers start: 38 outliers final: 34 residues processed: 320 average time/residue: 0.2067 time to fit residues: 89.0623 Evaluate side-chains 332 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 148 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 73 ARG 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 73 ARG Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127549 restraints weight = 19363.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129601 restraints weight = 9822.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130955 restraints weight = 6014.504| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8348 Z= 0.312 Angle : 0.897 11.279 11271 Z= 0.457 Chirality : 0.050 0.231 1255 Planarity : 0.005 0.079 1460 Dihedral : 5.549 38.910 1136 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.13 % Allowed : 30.20 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.28), residues: 1029 helix: 1.23 (0.23), residues: 594 sheet: -1.52 (0.57), residues: 81 loop : -3.32 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 95 HIS 0.004 0.001 HIS B 105 PHE 0.040 0.003 PHE D 109 TYR 0.016 0.002 TYR A 160 ARG 0.012 0.001 ARG D 15 =============================================================================== Job complete usr+sys time: 3823.49 seconds wall clock time: 69 minutes 4.73 seconds (4144.73 seconds total)