Starting phenix.real_space_refine on Fri Jun 5 04:23:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjx_60159/06_2026/8zjx_60159.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 11039 2.51 5 N 3001 2.21 5 O 3258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17386 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "B" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "D" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1605 Classifications: {'peptide': 205} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 188} Chain: "E" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2256 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 280} Chain: "F" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3832 Classifications: {'peptide': 484} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 458} Chain: "G" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1786 Classifications: {'peptide': 225} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.25 Number of scatterers: 17386 At special positions: 0 Unit cell: (142.204, 148.667, 290.871, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 3258 8.00 N 3001 7.00 C 11039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.05 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.05 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: 1.56 Conformation dependent library (CDL) restraints added in 839.8 milliseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4078 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 35 sheets defined 17.6% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 249 through 322 removed outlier: 4.108A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 3.813A pdb=" N LYS A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.824A pdb=" N ALA A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.536A pdb=" N GLU B 87 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.955A pdb=" N ARG B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.824A pdb=" N ASN B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 322 removed outlier: 3.598A pdb=" N ILE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Proline residue: B 261 - end of helix removed outlier: 3.648A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 245 through 254 Processing helix chain 'E' and resid 255 through 322 removed outlier: 3.612A pdb=" N LEU E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.922A pdb=" N ARG F 243 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 319 removed outlier: 4.224A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Proline residue: F 257 - end of helix removed outlier: 4.015A pdb=" N ARG F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 283 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 425 through 428 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.727A pdb=" N ILE G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.581A pdb=" N PHE A 67 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.007A pdb=" N VAL A 77 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 84 " --> pdb=" O VAL A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.249A pdb=" N PHE A 201 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.633A pdb=" N ALA A 186 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP A 178 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 343 removed outlier: 4.396A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 325 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 349 through 350 removed outlier: 4.218A pdb=" N LEU B 325 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 461 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 463 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AB1, first strand: chain 'B' and resid 31 through 33 removed outlier: 7.856A pdb=" N SER B 107 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS B 101 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AB3, first strand: chain 'B' and resid 150 through 156 removed outlier: 5.184A pdb=" N ARG B 162 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG B 162 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE B 209 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU B 164 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 207 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 190 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AB5, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.638A pdb=" N TRP B 398 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 431 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.638A pdb=" N PHE D 110 " --> pdb=" O CYS D 94 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS D 94 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS D 112 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N CYS D 92 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 135 removed outlier: 6.101A pdb=" N TYR D 176 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 129 through 135 removed outlier: 6.101A pdb=" N TYR D 176 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 156 removed outlier: 3.654A pdb=" N THR D 191 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 34 removed outlier: 7.055A pdb=" N LYS E 108 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP E 102 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 110 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 40 through 43 removed outlier: 5.948A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL E 78 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.706A pdb=" N VAL E 204 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR E 169 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA E 206 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG E 167 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 208 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU E 165 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET E 210 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N HIS E 163 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR E 157 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS E 163 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.417A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS F 163 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR F 157 " --> pdb=" O GLY F 161 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY F 161 " --> pdb=" O TYR F 157 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 40 through 43 removed outlier: 6.217A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 144 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA F 42 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL F 78 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.080A pdb=" N ALA F 110 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG F 101 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG F 112 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE F 99 " --> pdb=" O ARG F 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.820A pdb=" N VAL F 195 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 338 through 339 removed outlier: 5.854A pdb=" N ASN F 475 " --> pdb=" O HIS F 481 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS F 481 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 338 through 339 removed outlier: 3.674A pdb=" N THR F 509 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 353 through 355 Processing sheet with id=AD3, first strand: chain 'F' and resid 383 through 385 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.282A pdb=" N SER G 11 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR G 118 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS G 13 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 93 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.282A pdb=" N SER G 11 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR G 118 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS G 13 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 93 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 133 removed outlier: 3.594A pdb=" N LEU G 149 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR G 187 " --> pdb=" O LYS G 154 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 161 through 167 removed outlier: 4.253A pdb=" N GLU G 203 " --> pdb=" O LYS G 167 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2076 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: 3.59 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5724 1.34 - 1.47: 4060 1.47 - 1.59: 7865 1.59 - 1.71: 3 1.71 - 1.83: 125 Bond restraints: 17777 Sorted by residual: bond pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 1.697 1.645 0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " ideal model delta sigma weight residual 1.594 1.644 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C28 H6P F 601 " pdb=" O29 H6P F 601 " ideal model delta sigma weight residual 1.442 1.399 0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" C31 H6P F 601 " pdb=" O33 H6P F 601 " ideal model delta sigma weight residual 1.440 1.399 0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C27 H6P F 601 " pdb=" C28 H6P F 601 " ideal model delta sigma weight residual 1.495 1.524 -0.029 2.00e-02 2.50e+03 2.11e+00 ... (remaining 17772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 23801 2.25 - 4.51: 257 4.51 - 6.76: 16 6.76 - 9.02: 3 9.02 - 11.27: 5 Bond angle restraints: 24082 Sorted by residual: angle pdb=" C MET D 25 " pdb=" N LYS D 26 " pdb=" CA LYS D 26 " ideal model delta sigma weight residual 121.70 132.97 -11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" C GLY D 43 " pdb=" N ASN D 44 " pdb=" CA ASN D 44 " ideal model delta sigma weight residual 121.70 132.13 -10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" C LYS G 167 " pdb=" N LYS G 168 " pdb=" CA LYS G 168 " ideal model delta sigma weight residual 121.70 130.87 -9.17 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C GLU D 52 " pdb=" N LYS D 53 " pdb=" CA LYS D 53 " ideal model delta sigma weight residual 121.70 129.28 -7.58 1.80e+00 3.09e-01 1.77e+01 angle pdb=" P13 H6P F 601 " pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 135.28 124.58 10.70 3.00e+00 1.11e-01 1.27e+01 ... (remaining 24077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 10442 33.16 - 66.31: 317 66.31 - 99.47: 42 99.47 - 132.63: 0 132.63 - 165.78: 2 Dihedral angle restraints: 10803 sinusoidal: 4466 harmonic: 6337 Sorted by residual: dihedral pdb=" CB CYS B 51 " pdb=" SG CYS B 51 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual 93.00 -177.91 -89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS D 141 " pdb=" SG CYS D 141 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual 93.00 8.87 84.13 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 164.68 -71.68 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 10800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1490 0.029 - 0.057: 738 0.057 - 0.086: 188 0.086 - 0.115: 184 0.115 - 0.143: 53 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CA ILE D 151 " pdb=" N ILE D 151 " pdb=" C ILE D 151 " pdb=" CB ILE D 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE E 187 " pdb=" N ILE E 187 " pdb=" C ILE E 187 " pdb=" CB ILE E 187 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE D 79 " pdb=" N ILE D 79 " pdb=" C ILE D 79 " pdb=" CB ILE D 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2650 not shown) Planarity restraints: 3107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 241 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO B 242 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 242 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 242 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 192 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO E 193 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 193 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 193 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 186 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO A 187 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.033 5.00e-02 4.00e+02 ... (remaining 3104 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 275 2.63 - 3.20: 15487 3.20 - 3.76: 25432 3.76 - 4.33: 36722 4.33 - 4.90: 62078 Nonbonded interactions: 139994 Sorted by model distance: nonbonded pdb=" NE2 HIS B 156 " pdb=" O PHE B 240 " model vdw 2.061 3.120 nonbonded pdb=" O PRO A 149 " pdb=" OG SER A 232 " model vdw 2.080 3.040 nonbonded pdb=" NZ LYS A 212 " pdb=" O MET A 241 " model vdw 2.138 3.120 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR B 387 " model vdw 2.159 3.040 nonbonded pdb=" O CYS D 23 " pdb=" OG SER D 24 " model vdw 2.162 3.040 ... (remaining 139989 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 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 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: 0.400 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.610 Find NCS groups from input model: 0.200 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17791 Z= 0.157 Angle : 0.611 11.273 24110 Z= 0.321 Chirality : 0.044 0.143 2653 Planarity : 0.004 0.076 3107 Dihedral : 15.865 165.783 6683 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 0.05 % Allowed : 15.32 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2181 helix: 3.30 (0.28), residues: 309 sheet: -0.83 (0.18), residues: 766 loop : -1.24 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 300 TYR 0.020 0.001 TYR A 92 PHE 0.011 0.001 PHE G 156 TRP 0.019 0.001 TRP E 248 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (17777) covalent geometry : angle 0.60924 / 0.32 (24082) SS BOND : bond 0.00737 / 0.45 ( 14) SS BOND : angle 1.44969 / 0.85 ( 28) hydrogen bonds : bond 0.11250 / 7.37 ( 757) hydrogen bonds : angle 6.24666 / 4.31 ( 2076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 237 ILE cc_start: 0.5506 (mt) cc_final: 0.5035 (mt) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1472 time to fit residues: 44.4158 Evaluate side-chains 102 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.0010 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.7548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 74 GLN F 77 ASN F 326 HIS G 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.059506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.047527 restraints weight = 175246.850| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 5.31 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17791 Z= 0.157 Angle : 0.690 9.692 24110 Z= 0.353 Chirality : 0.046 0.201 2653 Planarity : 0.005 0.049 3107 Dihedral : 6.808 159.327 2409 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.83 % Allowed : 17.25 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2181 helix: 3.15 (0.28), residues: 311 sheet: -0.71 (0.17), residues: 802 loop : -1.12 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 300 TYR 0.019 0.002 TYR B 387 PHE 0.019 0.002 PHE B 127 TRP 0.020 0.002 TRP G 164 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (17777) covalent geometry : angle 0.68855 / 0.35 (24082) SS BOND : bond 0.00486 / 0.30 ( 14) SS BOND : angle 1.31939 / 0.77 ( 28) hydrogen bonds : bond 0.05005 / 3.28 ( 757) hydrogen bonds : angle 5.46556 / 3.76 ( 2076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6521 (ttm) REVERT: B 217 MET cc_start: 0.6433 (mmm) cc_final: 0.6219 (mmp) REVERT: D 184 TYR cc_start: 0.6023 (m-10) cc_final: 0.5820 (m-10) REVERT: E 210 MET cc_start: 0.4662 (mmm) cc_final: 0.4391 (mmm) REVERT: F 43 MET cc_start: 0.7114 (mmp) cc_final: 0.6555 (tpp) REVERT: F 210 MET cc_start: 0.6541 (ttt) cc_final: 0.6321 (tmm) REVERT: G 64 ILE cc_start: 0.6035 (pt) cc_final: 0.5542 (mt) outliers start: 35 outliers final: 14 residues processed: 148 average time/residue: 0.1162 time to fit residues: 27.2084 Evaluate side-chains 110 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain G residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 189 optimal weight: 0.0170 chunk 24 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 14 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.059094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.046866 restraints weight = 177780.686| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 5.14 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17791 Z= 0.130 Angle : 0.622 9.744 24110 Z= 0.317 Chirality : 0.044 0.175 2653 Planarity : 0.004 0.043 3107 Dihedral : 6.398 150.869 2409 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.14 % Allowed : 18.03 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2181 helix: 3.38 (0.28), residues: 303 sheet: -0.58 (0.17), residues: 810 loop : -0.97 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.014 0.001 TYR A 92 PHE 0.013 0.001 PHE B 127 TRP 0.021 0.001 TRP A 398 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (17777) covalent geometry : angle 0.62122 / 0.32 (24082) SS BOND : bond 0.00745 / 0.39 ( 14) SS BOND : angle 1.20434 / 0.71 ( 28) hydrogen bonds : bond 0.04554 / 2.99 ( 757) hydrogen bonds : angle 5.16512 / 3.56 ( 2076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.3461 (mtt) cc_final: 0.3046 (mtt) REVERT: D 184 TYR cc_start: 0.5838 (m-10) cc_final: 0.5595 (m-10) REVERT: E 181 ASN cc_start: 0.2324 (OUTLIER) cc_final: 0.2026 (t0) REVERT: E 210 MET cc_start: 0.4127 (mmm) cc_final: 0.3642 (mmm) REVERT: F 43 MET cc_start: 0.7260 (mmp) cc_final: 0.6774 (tpp) REVERT: F 100 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (pp) REVERT: F 210 MET cc_start: 0.6208 (ttt) cc_final: 0.5975 (tmm) REVERT: F 384 VAL cc_start: 0.7886 (t) cc_final: 0.7592 (p) outliers start: 41 outliers final: 15 residues processed: 142 average time/residue: 0.1206 time to fit residues: 27.0073 Evaluate side-chains 110 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 298 MET Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 193 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 125 HIS D 154 ASN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS F 178 GLN F 330 ASN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.055064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.043183 restraints weight = 180257.091| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 5.12 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 17791 Z= 0.217 Angle : 0.772 13.060 24110 Z= 0.397 Chirality : 0.047 0.197 2653 Planarity : 0.006 0.059 3107 Dihedral : 6.622 149.223 2409 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 2.56 % Allowed : 18.77 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2181 helix: 3.06 (0.28), residues: 306 sheet: -0.59 (0.17), residues: 814 loop : -1.09 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 121 TYR 0.030 0.002 TYR B 387 PHE 0.024 0.002 PHE B 453 TRP 0.028 0.003 TRP E 67 HIS 0.010 0.002 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (17777) covalent geometry : angle 0.77082 / 0.40 (24082) SS BOND : bond 0.00584 / 0.36 ( 14) SS BOND : angle 1.65646 / 0.99 ( 28) hydrogen bonds : bond 0.04860 / 3.15 ( 757) hydrogen bonds : angle 5.54172 / 3.81 ( 2076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.4932 (mtt) cc_final: 0.4547 (mtt) REVERT: B 317 GLU cc_start: 0.7991 (tt0) cc_final: 0.7683 (tm-30) REVERT: B 426 MET cc_start: 0.7733 (tpp) cc_final: 0.7526 (tpp) REVERT: B 473 TYR cc_start: 0.6682 (t80) cc_final: 0.5653 (t80) REVERT: D 87 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: D 181 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7612 (pp) REVERT: E 293 MET cc_start: 0.9014 (ptp) cc_final: 0.8814 (ptp) REVERT: F 100 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (pp) REVERT: F 298 MET cc_start: 0.8467 (tpt) cc_final: 0.8195 (tpt) REVERT: F 433 MET cc_start: 0.7224 (tmm) cc_final: 0.6893 (tmm) outliers start: 49 outliers final: 20 residues processed: 133 average time/residue: 0.1225 time to fit residues: 25.7088 Evaluate side-chains 104 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS D 36 ASN F 374 ASN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.053037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.040943 restraints weight = 174772.175| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.56 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17791 Z= 0.205 Angle : 0.664 9.218 24110 Z= 0.343 Chirality : 0.045 0.196 2653 Planarity : 0.004 0.047 3107 Dihedral : 6.325 144.272 2409 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.93 % Allowed : 20.39 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2181 helix: 3.32 (0.28), residues: 306 sheet: -0.53 (0.17), residues: 811 loop : -1.01 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 287 TYR 0.016 0.002 TYR G 36 PHE 0.014 0.002 PHE B 67 TRP 0.015 0.002 TRP E 67 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (17777) covalent geometry : angle 0.65997 / 0.34 (24082) SS BOND : bond 0.00709 / 0.38 ( 14) SS BOND : angle 2.33685 / 1.38 ( 28) hydrogen bonds : bond 0.04234 / 2.79 ( 757) hydrogen bonds : angle 5.18566 / 3.57 ( 2076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7800 (mtm) cc_final: 0.7397 (mtm) REVERT: A 241 MET cc_start: 0.5272 (mtt) cc_final: 0.4842 (mtt) REVERT: B 62 MET cc_start: 0.8258 (tpp) cc_final: 0.7926 (tpp) REVERT: B 317 GLU cc_start: 0.8025 (tt0) cc_final: 0.7740 (tm-30) REVERT: B 426 MET cc_start: 0.7031 (tpp) cc_final: 0.6792 (tpp) REVERT: B 473 TYR cc_start: 0.7094 (t80) cc_final: 0.6017 (t80) REVERT: E 293 MET cc_start: 0.8905 (ptp) cc_final: 0.8671 (ptp) REVERT: F 58 MET cc_start: 0.8381 (pmm) cc_final: 0.7976 (pmm) REVERT: F 100 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7877 (pp) REVERT: F 207 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8754 (t) REVERT: F 374 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8310 (p0) REVERT: G 188 MET cc_start: 0.7559 (ptt) cc_final: 0.7063 (ptt) outliers start: 37 outliers final: 23 residues processed: 112 average time/residue: 0.1290 time to fit residues: 22.6472 Evaluate side-chains 95 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 140 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN E 77 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.050527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.038156 restraints weight = 164397.382| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 5.17 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.9699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 17791 Z= 0.284 Angle : 0.773 11.003 24110 Z= 0.399 Chirality : 0.047 0.231 2653 Planarity : 0.006 0.060 3107 Dihedral : 6.852 149.347 2409 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.61 % Allowed : 20.81 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2181 helix: 2.80 (0.28), residues: 307 sheet: -0.71 (0.17), residues: 828 loop : -1.05 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 300 TYR 0.022 0.002 TYR F 202 PHE 0.020 0.002 PHE B 453 TRP 0.026 0.002 TRP D 37 HIS 0.008 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.28 (17777) covalent geometry : angle 0.77156 / 0.40 (24082) SS BOND : bond 0.00540 / 0.35 ( 14) SS BOND : angle 1.68820 / 0.99 ( 28) hydrogen bonds : bond 0.04731 / 3.11 ( 757) hydrogen bonds : angle 5.64482 / 3.88 ( 2076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 65 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6104 (mtt) cc_final: 0.5728 (mtt) REVERT: B 241 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6931 (ttt) REVERT: B 426 MET cc_start: 0.7287 (tpp) cc_final: 0.7072 (tpp) REVERT: F 58 MET cc_start: 0.8703 (pmm) cc_final: 0.8393 (pmm) REVERT: F 100 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8363 (pp) REVERT: F 211 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7393 (mtp85) REVERT: F 298 MET cc_start: 0.8926 (tpt) cc_final: 0.8483 (tpt) REVERT: F 403 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8080 (m-30) outliers start: 50 outliers final: 25 residues processed: 112 average time/residue: 0.1313 time to fit residues: 22.9453 Evaluate side-chains 88 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 215 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 147 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.050618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.038362 restraints weight = 162249.084| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.10 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 1.0068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17791 Z= 0.168 Angle : 0.641 12.508 24110 Z= 0.327 Chirality : 0.044 0.156 2653 Planarity : 0.004 0.044 3107 Dihedral : 6.534 148.837 2409 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.83 % Allowed : 21.75 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2181 helix: 3.13 (0.28), residues: 306 sheet: -0.59 (0.17), residues: 824 loop : -0.93 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 121 TYR 0.014 0.001 TYR B 126 PHE 0.016 0.001 PHE E 55 TRP 0.013 0.001 TRP F 67 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17777) covalent geometry : angle 0.63967 / 0.33 (24082) SS BOND : bond 0.00591 / 0.40 ( 14) SS BOND : angle 1.45920 / 0.85 ( 28) hydrogen bonds : bond 0.04163 / 2.75 ( 757) hydrogen bonds : angle 5.28137 / 3.63 ( 2076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8077 (mtm) cc_final: 0.7654 (mpp) REVERT: A 241 MET cc_start: 0.6166 (mtt) cc_final: 0.5808 (mtt) REVERT: B 62 MET cc_start: 0.8794 (tpp) cc_final: 0.8476 (tpp) REVERT: B 202 MET cc_start: 0.8800 (tpp) cc_final: 0.8501 (tpp) REVERT: B 426 MET cc_start: 0.6849 (tpp) cc_final: 0.6575 (tpp) REVERT: D 185 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8121 (mt-10) REVERT: F 58 MET cc_start: 0.8641 (pmm) cc_final: 0.8386 (pmm) REVERT: F 100 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8342 (pp) REVERT: F 207 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8730 (t) REVERT: G 54 TYR cc_start: 0.9026 (p90) cc_final: 0.8814 (p90) outliers start: 35 outliers final: 21 residues processed: 96 average time/residue: 0.1326 time to fit residues: 19.7305 Evaluate side-chains 85 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 141 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 5 optimal weight: 0.0270 chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.049578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.037056 restraints weight = 159677.065| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.09 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 1.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17791 Z= 0.208 Angle : 0.692 12.368 24110 Z= 0.350 Chirality : 0.045 0.298 2653 Planarity : 0.004 0.059 3107 Dihedral : 6.576 148.289 2409 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.83 % Allowed : 21.80 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2181 helix: 3.06 (0.28), residues: 307 sheet: -0.59 (0.17), residues: 821 loop : -0.98 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 300 TYR 0.015 0.002 TYR F 202 PHE 0.015 0.002 PHE B 453 TRP 0.014 0.002 TRP E 67 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (17777) covalent geometry : angle 0.69016 / 0.35 (24082) SS BOND : bond 0.00482 / 0.30 ( 14) SS BOND : angle 1.64189 / 0.97 ( 28) hydrogen bonds : bond 0.04246 / 2.82 ( 757) hydrogen bonds : angle 5.35238 / 3.69 ( 2076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7857 (mtm) cc_final: 0.7365 (mpp) REVERT: A 241 MET cc_start: 0.6593 (mtt) cc_final: 0.6230 (mtt) REVERT: A 259 MET cc_start: 0.6832 (tpt) cc_final: 0.6623 (tpt) REVERT: B 426 MET cc_start: 0.6993 (tpp) cc_final: 0.6743 (tpp) REVERT: B 466 MET cc_start: 0.7944 (mmm) cc_final: 0.7732 (mmm) REVERT: D 185 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7973 (mt-10) REVERT: E 293 MET cc_start: 0.8953 (ptp) cc_final: 0.8686 (ptp) REVERT: F 58 MET cc_start: 0.8696 (pmm) cc_final: 0.8223 (pmm) REVERT: F 63 MET cc_start: 0.1386 (OUTLIER) cc_final: 0.0783 (ptp) REVERT: F 100 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8233 (pp) outliers start: 35 outliers final: 23 residues processed: 94 average time/residue: 0.1428 time to fit residues: 21.0329 Evaluate side-chains 82 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 21 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 151 optimal weight: 0.0770 chunk 179 optimal weight: 0.0570 chunk 188 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN D 44 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.050276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.038137 restraints weight = 159711.766| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 5.22 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 1.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17791 Z= 0.123 Angle : 0.629 13.143 24110 Z= 0.315 Chirality : 0.044 0.174 2653 Planarity : 0.004 0.045 3107 Dihedral : 6.340 147.873 2409 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.20 % Allowed : 22.58 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2181 helix: 3.20 (0.28), residues: 306 sheet: -0.37 (0.18), residues: 802 loop : -0.89 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 121 TYR 0.017 0.001 TYR G 54 PHE 0.011 0.001 PHE B 67 TRP 0.012 0.001 TRP A 398 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17777) covalent geometry : angle 0.62833 / 0.31 (24082) SS BOND : bond 0.00421 / 0.26 ( 14) SS BOND : angle 1.27465 / 0.74 ( 28) hydrogen bonds : bond 0.03894 / 2.58 ( 757) hydrogen bonds : angle 5.08526 / 3.50 ( 2076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8089 (mtm) cc_final: 0.7595 (mpp) REVERT: A 241 MET cc_start: 0.6567 (mtt) cc_final: 0.5698 (ptp) REVERT: B 426 MET cc_start: 0.7127 (tpp) cc_final: 0.6875 (tpp) REVERT: D 185 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8069 (mt-10) REVERT: E 58 MET cc_start: 0.8772 (pmm) cc_final: 0.8544 (pmm) REVERT: F 58 MET cc_start: 0.8710 (pmm) cc_final: 0.8382 (pmm) REVERT: F 433 MET cc_start: 0.8031 (tmm) cc_final: 0.7827 (tmm) outliers start: 23 outliers final: 19 residues processed: 85 average time/residue: 0.1425 time to fit residues: 18.7010 Evaluate side-chains 76 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 189 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.050194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.037685 restraints weight = 158806.984| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 5.11 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 1.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17791 Z= 0.129 Angle : 0.640 13.216 24110 Z= 0.319 Chirality : 0.044 0.170 2653 Planarity : 0.004 0.046 3107 Dihedral : 6.260 147.113 2409 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.15 % Allowed : 22.63 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2181 helix: 3.29 (0.28), residues: 306 sheet: -0.32 (0.18), residues: 805 loop : -0.81 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 300 TYR 0.011 0.001 TYR B 126 PHE 0.010 0.001 PHE A 76 TRP 0.010 0.001 TRP B 398 HIS 0.004 0.001 HIS F 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17777) covalent geometry : angle 0.63927 / 0.32 (24082) SS BOND : bond 0.00418 / 0.25 ( 14) SS BOND : angle 1.31481 / 0.77 ( 28) hydrogen bonds : bond 0.03866 / 2.55 ( 757) hydrogen bonds : angle 5.04144 / 3.47 ( 2076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8176 (mmp) cc_final: 0.7597 (pmm) REVERT: A 202 MET cc_start: 0.8010 (mtm) cc_final: 0.6329 (mpp) REVERT: A 241 MET cc_start: 0.6669 (mtt) cc_final: 0.5804 (ptp) REVERT: B 202 MET cc_start: 0.8886 (tpp) cc_final: 0.8453 (tpp) REVERT: B 426 MET cc_start: 0.7075 (tpp) cc_final: 0.6826 (tpp) REVERT: F 58 MET cc_start: 0.8616 (pmm) cc_final: 0.8277 (pmm) REVERT: F 242 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: G 121 GLN cc_start: 0.8972 (mp10) cc_final: 0.8711 (mp10) outliers start: 22 outliers final: 20 residues processed: 81 average time/residue: 0.1472 time to fit residues: 18.2765 Evaluate side-chains 78 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 0.0980 chunk 206 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 HIS ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.050156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.037684 restraints weight = 160400.085| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.11 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 1.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17791 Z= 0.128 Angle : 0.634 13.149 24110 Z= 0.316 Chirality : 0.044 0.183 2653 Planarity : 0.004 0.069 3107 Dihedral : 6.191 145.486 2409 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.20 % Allowed : 22.48 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.74 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2181 helix: 3.28 (0.28), residues: 306 sheet: -0.29 (0.18), residues: 814 loop : -0.76 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 305 TYR 0.011 0.001 TYR B 126 PHE 0.009 0.001 PHE B 67 TRP 0.012 0.001 TRP F 295 HIS 0.004 0.001 HIS F 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17777) covalent geometry : angle 0.63300 / 0.32 (24082) SS BOND : bond 0.00415 / 0.25 ( 14) SS BOND : angle 1.29097 / 0.76 ( 28) hydrogen bonds : bond 0.03860 / 2.55 ( 757) hydrogen bonds : angle 4.99186 / 3.43 ( 2076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4379.74 seconds wall clock time: 75 minutes 53.61 seconds (4553.61 seconds total)