Starting phenix.real_space_refine on Tue Aug 26 12:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld0_23278/08_2025/7ld0_23278.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 23416 2.51 5 N 6664 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "E" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "F" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "G" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "H" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Time building chain proxies: 8.38, per 1000 atoms: 0.23 Number of scatterers: 36976 At special positions: 0 Unit cell: (206.01, 206.01, 82.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 6744 8.00 N 6664 7.00 C 23416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 8 sheets defined 72.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.965A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.834A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS A 628 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.683A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.527A pdb=" N SER B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS B 628 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 104 removed outlier: 3.520A pdb=" N ALA C 93 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 101 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.811A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.534A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 359 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.836A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 477 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.658A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG C 535 " --> pdb=" O LEU C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS C 628 " --> pdb=" O ALA C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 283 through 289 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 309' Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 521 through 526 Processing helix chain 'D' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER D 578 " --> pdb=" O SER D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 3.856A pdb=" N MET D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS D 628 " --> pdb=" O ALA D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS D 649 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.871A pdb=" N ALA E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.681A pdb=" N LEU E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 289 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 359 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 430 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 477 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.730A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.656A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.611A pdb=" N ARG E 535 " --> pdb=" O LEU E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.636A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 614 " --> pdb=" O SER E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS E 628 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG E 697 " --> pdb=" O GLU E 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA F 309 " --> pdb=" O PRO F 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 304 through 309' Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.503A pdb=" N GLN F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 359 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 430 through 437 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG F 535 " --> pdb=" O LEU F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER F 578 " --> pdb=" O SER F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS F 628 " --> pdb=" O ALA F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS F 649 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG F 697 " --> pdb=" O GLU F 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 3.873A pdb=" N ALA G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN G 114 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 141 through 151 removed outlier: 4.169A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 309 " --> pdb=" O PRO G 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 309' Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 359 Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 413 through 423 Processing helix chain 'G' and resid 430 through 437 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 477 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 Processing helix chain 'G' and resid 521 through 526 Processing helix chain 'G' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER G 578 " --> pdb=" O SER G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS G 628 " --> pdb=" O ALA G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG G 697 " --> pdb=" O GLU G 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA H 93 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU H 101 " --> pdb=" O GLN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 283 through 289 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA H 309 " --> pdb=" O PRO H 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 304 through 309' Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.505A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 359 Processing helix chain 'H' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP H 367 " --> pdb=" O LYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 430 through 437 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 Processing helix chain 'H' and resid 521 through 526 Processing helix chain 'H' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG H 535 " --> pdb=" O LEU H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER H 578 " --> pdb=" O SER H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS H 628 " --> pdb=" O ALA H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 681 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 681 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 681 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 681 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 681 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 681 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 681 " --> pdb=" O PRO G 655 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 681 " --> pdb=" O PRO H 655 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5574 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: 7.92 Time building geometry restraints manager: 4.36 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: 12508 1.34 - 1.46: 5545 1.46 - 1.58: 19307 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 37552 Sorted by residual: bond pdb=" N ILE D 608 " pdb=" CA ILE D 608 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.51e+00 bond pdb=" N VAL B 611 " pdb=" CA VAL B 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.46e+00 bond pdb=" N ILE E 608 " pdb=" CA ILE E 608 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" CA SER D 381 " pdb=" CB SER D 381 " ideal model delta sigma weight residual 1.530 1.489 0.040 1.48e-02 4.57e+03 7.41e+00 bond pdb=" N VAL C 611 " pdb=" CA VAL C 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 37547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 48380 1.35 - 2.70: 1880 2.70 - 4.05: 390 4.05 - 5.40: 54 5.40 - 6.75: 24 Bond angle restraints: 50728 Sorted by residual: angle pdb=" CA SER F 77 " pdb=" C SER F 77 " pdb=" O SER F 77 " ideal model delta sigma weight residual 122.14 117.34 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" N ALA F 78 " pdb=" CA ALA F 78 " pdb=" C ALA F 78 " ideal model delta sigma weight residual 112.86 108.21 4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" N VAL H 611 " pdb=" CA VAL H 611 " pdb=" C VAL H 611 " ideal model delta sigma weight residual 110.62 106.80 3.82 1.02e+00 9.61e-01 1.40e+01 angle pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" C LEU A 607 " ideal model delta sigma weight residual 111.28 107.33 3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA ALA B 78 " pdb=" C ALA B 78 " pdb=" O ALA B 78 " ideal model delta sigma weight residual 120.32 116.09 4.23 1.18e+00 7.18e-01 1.29e+01 ... (remaining 50723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 20467 17.03 - 34.06: 2026 34.06 - 51.09: 273 51.09 - 68.13: 42 68.13 - 85.16: 32 Dihedral angle restraints: 22840 sinusoidal: 9296 harmonic: 13544 Sorted by residual: dihedral pdb=" CA THR B 140 " pdb=" C THR B 140 " pdb=" N ARG B 141 " pdb=" CA ARG B 141 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA THR C 140 " pdb=" C THR C 140 " pdb=" N ARG C 141 " pdb=" CA ARG C 141 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR E 140 " pdb=" C THR E 140 " pdb=" N ARG E 141 " pdb=" CA ARG E 141 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 22837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4832 0.051 - 0.102: 866 0.102 - 0.153: 122 0.153 - 0.203: 23 0.203 - 0.254: 5 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CA LEU A 607 " pdb=" N LEU A 607 " pdb=" C LEU A 607 " pdb=" CB LEU A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU D 607 " pdb=" N LEU D 607 " pdb=" C LEU D 607 " pdb=" CB LEU D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU B 607 " pdb=" N LEU B 607 " pdb=" C LEU B 607 " pdb=" CB LEU B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5845 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 79 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU D 79 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU D 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS D 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 79 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU C 79 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU C 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 79 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LEU E 79 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU E 79 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS E 80 " -0.022 2.00e-02 2.50e+03 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7152 2.76 - 3.30: 38646 3.30 - 3.83: 57420 3.83 - 4.37: 70395 4.37 - 4.90: 115408 Nonbonded interactions: 289021 Sorted by model distance: nonbonded pdb=" N VAL C 61 " pdb=" OD1 ASP C 63 " model vdw 2.229 3.120 nonbonded pdb=" N VAL H 61 " pdb=" OD1 ASP H 63 " model vdw 2.229 3.120 nonbonded pdb=" N VAL F 61 " pdb=" OD1 ASP F 63 " model vdw 2.229 3.120 nonbonded pdb=" N VAL A 61 " pdb=" OD1 ASP A 63 " model vdw 2.230 3.120 nonbonded pdb=" N VAL E 61 " pdb=" OD1 ASP E 63 " model vdw 2.230 3.120 ... (remaining 289016 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 34.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.006 0.040 37552 Z= 0.289 Angle : 0.651 6.745 50728 Z= 0.405 Chirality : 0.040 0.254 5848 Planarity : 0.006 0.049 6536 Dihedral : 13.277 85.157 14040 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.12), residues: 4624 helix: -0.77 (0.09), residues: 3040 sheet: -3.47 (0.29), residues: 144 loop : -2.19 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 569 TYR 0.011 0.001 TYR A 380 PHE 0.010 0.001 PHE G 476 TRP 0.025 0.002 TRP H 638 HIS 0.004 0.001 HIS H 583 Details of bonding type rmsd covalent geometry : bond 0.00573 (37552) covalent geometry : angle 0.65135 (50728) hydrogen bonds : bond 0.28345 ( 1882) hydrogen bonds : angle 8.42743 ( 5574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1119 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7832 (m110) cc_final: 0.7623 (m-40) REVERT: A 157 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8143 (mtm110) REVERT: A 196 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 197 GLU cc_start: 0.6824 (mp0) cc_final: 0.6576 (mp0) REVERT: A 264 GLU cc_start: 0.6619 (mp0) cc_final: 0.6401 (mp0) REVERT: A 380 TYR cc_start: 0.8093 (m-80) cc_final: 0.7810 (m-80) REVERT: A 495 ASP cc_start: 0.7405 (t0) cc_final: 0.7163 (t0) REVERT: A 520 GLU cc_start: 0.6716 (tp30) cc_final: 0.6400 (tp30) REVERT: A 589 PHE cc_start: 0.8304 (m-10) cc_final: 0.8092 (m-10) REVERT: A 609 GLN cc_start: 0.7973 (tp40) cc_final: 0.7484 (tp40) REVERT: A 682 LYS cc_start: 0.6846 (tptp) cc_final: 0.6489 (tptp) REVERT: A 694 LYS cc_start: 0.8372 (tmtt) cc_final: 0.8092 (tptp) REVERT: B 156 ASN cc_start: 0.7883 (m110) cc_final: 0.7529 (m-40) REVERT: B 197 GLU cc_start: 0.6913 (mp0) cc_final: 0.6692 (mp0) REVERT: B 201 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7579 (ttp80) REVERT: B 212 LEU cc_start: 0.8381 (mt) cc_final: 0.7866 (mt) REVERT: B 215 CYS cc_start: 0.7152 (m) cc_final: 0.6845 (m) REVERT: B 246 VAL cc_start: 0.8417 (t) cc_final: 0.8210 (t) REVERT: B 340 GLU cc_start: 0.7718 (mp0) cc_final: 0.7397 (mp0) REVERT: B 352 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 378 VAL cc_start: 0.7007 (p) cc_final: 0.6731 (m) REVERT: B 458 LYS cc_start: 0.7293 (mmpt) cc_final: 0.7078 (mmpt) REVERT: B 459 SER cc_start: 0.8326 (t) cc_final: 0.8061 (p) REVERT: B 495 ASP cc_start: 0.7562 (t0) cc_final: 0.7357 (t0) REVERT: B 520 GLU cc_start: 0.6793 (tp30) cc_final: 0.6560 (tp30) REVERT: B 565 PHE cc_start: 0.7501 (t80) cc_final: 0.7182 (t80) REVERT: B 694 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7726 (tptp) REVERT: C 100 GLU cc_start: 0.7794 (mp0) cc_final: 0.7541 (mp0) REVERT: C 197 GLU cc_start: 0.6895 (mp0) cc_final: 0.6629 (mp0) REVERT: C 286 GLU cc_start: 0.6783 (tp30) cc_final: 0.6521 (tp30) REVERT: C 520 GLU cc_start: 0.6843 (tp30) cc_final: 0.6473 (tp30) REVERT: C 526 ASP cc_start: 0.6948 (m-30) cc_final: 0.6740 (m-30) REVERT: C 589 PHE cc_start: 0.8064 (m-10) cc_final: 0.7765 (m-10) REVERT: C 682 LYS cc_start: 0.7159 (tptp) cc_final: 0.6848 (tptp) REVERT: C 686 GLU cc_start: 0.7375 (pp20) cc_final: 0.7060 (pp20) REVERT: C 694 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7619 (tptt) REVERT: D 156 ASN cc_start: 0.7899 (m110) cc_final: 0.7606 (m-40) REVERT: D 197 GLU cc_start: 0.6872 (mp0) cc_final: 0.6605 (mp0) REVERT: D 201 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7455 (ttp80) REVERT: D 261 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7528 (mmtp) REVERT: D 271 CYS cc_start: 0.6014 (m) cc_final: 0.5728 (m) REVERT: D 340 GLU cc_start: 0.7751 (mp0) cc_final: 0.7463 (mp0) REVERT: D 352 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7293 (mm-30) REVERT: D 378 VAL cc_start: 0.6769 (p) cc_final: 0.6394 (m) REVERT: D 383 ASN cc_start: 0.7489 (t0) cc_final: 0.7196 (t0) REVERT: D 454 ASP cc_start: 0.7645 (m-30) cc_final: 0.7413 (m-30) REVERT: D 565 PHE cc_start: 0.7692 (t80) cc_final: 0.7449 (t80) REVERT: D 609 GLN cc_start: 0.8127 (tp40) cc_final: 0.7814 (tp40) REVERT: D 682 LYS cc_start: 0.6966 (tptp) cc_final: 0.6505 (tptp) REVERT: D 694 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7644 (tptt) REVERT: D 695 ILE cc_start: 0.8223 (pt) cc_final: 0.7970 (pt) REVERT: E 71 GLU cc_start: 0.7281 (pm20) cc_final: 0.6908 (pm20) REVERT: E 143 GLN cc_start: 0.7454 (mp10) cc_final: 0.7127 (mp10) REVERT: E 157 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8105 (mtm110) REVERT: E 189 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6685 (tm-30) REVERT: E 609 GLN cc_start: 0.8180 (tp40) cc_final: 0.7882 (tp40) REVERT: F 156 ASN cc_start: 0.7565 (m110) cc_final: 0.7172 (m110) REVERT: F 159 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7899 (tpt90) REVERT: F 189 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6975 (tm-30) REVERT: F 197 GLU cc_start: 0.6807 (mp0) cc_final: 0.6543 (mp0) REVERT: F 201 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7413 (mtm180) REVERT: F 215 CYS cc_start: 0.7067 (m) cc_final: 0.6793 (m) REVERT: F 219 ASP cc_start: 0.6928 (t70) cc_final: 0.6698 (t0) REVERT: F 340 GLU cc_start: 0.7768 (mp0) cc_final: 0.7563 (mp0) REVERT: F 352 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7198 (mm-30) REVERT: F 378 VAL cc_start: 0.6750 (p) cc_final: 0.6283 (m) REVERT: F 454 ASP cc_start: 0.7568 (m-30) cc_final: 0.7338 (m-30) REVERT: F 458 LYS cc_start: 0.7123 (mmpt) cc_final: 0.6915 (mmpt) REVERT: F 609 GLN cc_start: 0.8007 (tp40) cc_final: 0.7557 (tp40) REVERT: G 100 GLU cc_start: 0.7753 (mp0) cc_final: 0.7496 (mp0) REVERT: G 143 GLN cc_start: 0.7546 (mp10) cc_final: 0.7213 (mp10) REVERT: G 153 VAL cc_start: 0.7616 (t) cc_final: 0.7380 (t) REVERT: G 189 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7043 (tm-30) REVERT: G 197 GLU cc_start: 0.6720 (mp0) cc_final: 0.6502 (mp0) REVERT: G 391 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7499 (ttmm) REVERT: G 452 GLN cc_start: 0.8052 (tt0) cc_final: 0.7590 (tt0) REVERT: G 516 HIS cc_start: 0.8146 (p90) cc_final: 0.7703 (p90) REVERT: G 520 GLU cc_start: 0.6772 (tp30) cc_final: 0.6475 (tp30) REVERT: G 609 GLN cc_start: 0.7971 (tp40) cc_final: 0.7561 (tp40) REVERT: G 694 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8012 (tmtt) REVERT: H 100 GLU cc_start: 0.7888 (mp0) cc_final: 0.7622 (mp0) REVERT: H 156 ASN cc_start: 0.7776 (m110) cc_final: 0.7354 (m110) REVERT: H 189 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7066 (tm-30) REVERT: H 197 GLU cc_start: 0.6877 (mp0) cc_final: 0.6654 (mp0) REVERT: H 246 VAL cc_start: 0.8286 (t) cc_final: 0.8076 (t) REVERT: H 253 TRP cc_start: 0.7834 (m100) cc_final: 0.7320 (m100) REVERT: H 340 GLU cc_start: 0.7678 (mp0) cc_final: 0.7237 (mp0) REVERT: H 352 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7175 (mm-30) REVERT: H 378 VAL cc_start: 0.6941 (p) cc_final: 0.6634 (m) REVERT: H 450 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6430 (mt-10) REVERT: H 454 ASP cc_start: 0.7645 (m-30) cc_final: 0.7392 (m-30) REVERT: H 458 LYS cc_start: 0.7241 (mmpt) cc_final: 0.7037 (mmpt) REVERT: H 495 ASP cc_start: 0.7561 (t0) cc_final: 0.7318 (t0) REVERT: H 592 PHE cc_start: 0.7401 (t80) cc_final: 0.7082 (t80) REVERT: H 694 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7900 (tptt) outliers start: 0 outliers final: 0 residues processed: 1119 average time/residue: 0.2687 time to fit residues: 461.6760 Evaluate side-chains 1041 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1041 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 522 GLN B 156 ASN B 232 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN C 156 ASN C 437 GLN C 534 HIS C 571 ASN D 156 ASN D 232 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 ASN E 156 ASN F 156 ASN ** F 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS G 156 ASN G 522 GLN H 156 ASN H 232 ASN H 383 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.155850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130904 restraints weight = 55146.126| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.24 r_work: 0.3558 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37552 Z= 0.176 Angle : 0.705 10.753 50728 Z= 0.356 Chirality : 0.044 0.222 5848 Planarity : 0.005 0.049 6536 Dihedral : 4.598 23.557 5128 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.45 % Allowed : 12.30 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.12), residues: 4624 helix: 0.02 (0.09), residues: 3168 sheet: -3.31 (0.31), residues: 160 loop : -2.01 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 484 TYR 0.010 0.001 TYR E 503 PHE 0.023 0.002 PHE C 565 TRP 0.012 0.002 TRP A 103 HIS 0.012 0.001 HIS E 587 Details of bonding type rmsd covalent geometry : bond 0.00388 (37552) covalent geometry : angle 0.70471 (50728) hydrogen bonds : bond 0.06145 ( 1882) hydrogen bonds : angle 5.10004 ( 5574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1080 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7150 (mp0) cc_final: 0.6829 (mp0) REVERT: A 189 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 195 SER cc_start: 0.7955 (m) cc_final: 0.7477 (t) REVERT: A 197 GLU cc_start: 0.7126 (mp0) cc_final: 0.6728 (mp0) REVERT: A 495 ASP cc_start: 0.7778 (t0) cc_final: 0.7471 (t0) REVERT: A 520 GLU cc_start: 0.7042 (tp30) cc_final: 0.6840 (tp30) REVERT: A 609 GLN cc_start: 0.8173 (tp40) cc_final: 0.7593 (tp40) REVERT: A 682 LYS cc_start: 0.6966 (tptp) cc_final: 0.6612 (tptp) REVERT: A 694 LYS cc_start: 0.8382 (tmtt) cc_final: 0.7895 (tptp) REVERT: A 695 ILE cc_start: 0.8775 (pt) cc_final: 0.8549 (pt) REVERT: B 156 ASN cc_start: 0.7716 (m-40) cc_final: 0.7457 (m110) REVERT: B 212 LEU cc_start: 0.8392 (mt) cc_final: 0.8158 (mp) REVERT: B 219 ASP cc_start: 0.7069 (t70) cc_final: 0.6834 (t0) REVERT: B 352 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 459 SER cc_start: 0.8529 (t) cc_final: 0.8307 (p) REVERT: B 497 ARG cc_start: 0.7550 (mtm180) cc_final: 0.7257 (ptp-170) REVERT: B 520 GLU cc_start: 0.7216 (tp30) cc_final: 0.6880 (tp30) REVERT: B 540 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8354 (t) REVERT: B 694 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7804 (tptt) REVERT: C 100 GLU cc_start: 0.7927 (mp0) cc_final: 0.7645 (mp0) REVERT: C 149 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7277 (mm-30) REVERT: C 189 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7449 (tm-30) REVERT: C 195 SER cc_start: 0.7864 (m) cc_final: 0.7367 (t) REVERT: C 197 GLU cc_start: 0.7151 (mp0) cc_final: 0.6771 (mp0) REVERT: C 286 GLU cc_start: 0.7371 (tp30) cc_final: 0.7102 (tp30) REVERT: C 413 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7599 (mtpp) REVERT: C 520 GLU cc_start: 0.7196 (tp30) cc_final: 0.6967 (tp30) REVERT: C 682 LYS cc_start: 0.7222 (tptp) cc_final: 0.6894 (tptp) REVERT: C 686 GLU cc_start: 0.7669 (pp20) cc_final: 0.7333 (pp20) REVERT: C 694 LYS cc_start: 0.7955 (tmtt) cc_final: 0.7591 (tptt) REVERT: D 156 ASN cc_start: 0.7964 (m-40) cc_final: 0.7646 (m-40) REVERT: D 157 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7835 (mtm110) REVERT: D 191 MET cc_start: 0.8043 (mmp) cc_final: 0.7768 (mmp) REVERT: D 195 SER cc_start: 0.8028 (m) cc_final: 0.7533 (t) REVERT: D 196 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6827 (tm-30) REVERT: D 197 GLU cc_start: 0.7211 (mp0) cc_final: 0.6866 (mp0) REVERT: D 249 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7622 (mtt90) REVERT: D 286 GLU cc_start: 0.7182 (tp30) cc_final: 0.6911 (tp30) REVERT: D 340 GLU cc_start: 0.7844 (mp0) cc_final: 0.7603 (mp0) REVERT: D 352 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 454 ASP cc_start: 0.7864 (m-30) cc_final: 0.7610 (m-30) REVERT: D 540 THR cc_start: 0.8577 (p) cc_final: 0.8364 (t) REVERT: D 565 PHE cc_start: 0.7900 (t80) cc_final: 0.7615 (t80) REVERT: D 682 LYS cc_start: 0.7051 (tptp) cc_final: 0.6605 (tptp) REVERT: D 694 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7589 (tptt) REVERT: D 695 ILE cc_start: 0.8493 (pt) cc_final: 0.8202 (pt) REVERT: E 189 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 196 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6319 (tm-30) REVERT: E 349 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (mp) REVERT: E 444 LEU cc_start: 0.8660 (mp) cc_final: 0.8446 (mt) REVERT: E 609 GLN cc_start: 0.8396 (tp40) cc_final: 0.8078 (tp40) REVERT: F 156 ASN cc_start: 0.7499 (m-40) cc_final: 0.7141 (m-40) REVERT: F 189 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7444 (tm-30) REVERT: F 197 GLU cc_start: 0.7195 (mp0) cc_final: 0.6840 (mp0) REVERT: F 201 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7738 (mtm110) REVERT: F 212 LEU cc_start: 0.8414 (mt) cc_final: 0.7842 (mp) REVERT: F 215 CYS cc_start: 0.7513 (m) cc_final: 0.7128 (m) REVERT: F 282 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: F 352 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7476 (mm-30) REVERT: F 450 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6465 (mt-10) REVERT: F 454 ASP cc_start: 0.7850 (m-30) cc_final: 0.7587 (m-30) REVERT: F 540 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (t) REVERT: F 609 GLN cc_start: 0.8045 (tp40) cc_final: 0.7427 (tp40) REVERT: F 612 MET cc_start: 0.7631 (tpp) cc_final: 0.6992 (tpp) REVERT: F 681 ILE cc_start: 0.7167 (mp) cc_final: 0.6913 (mp) REVERT: F 694 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7685 (tptt) REVERT: G 100 GLU cc_start: 0.7793 (mp0) cc_final: 0.7517 (mp0) REVERT: G 111 GLU cc_start: 0.7521 (tp30) cc_final: 0.7219 (tp30) REVERT: G 189 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7465 (tm-30) REVERT: G 195 SER cc_start: 0.7800 (m) cc_final: 0.7430 (t) REVERT: G 196 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6657 (tm-30) REVERT: G 197 GLU cc_start: 0.7024 (mp0) cc_final: 0.6762 (mp0) REVERT: G 376 ARG cc_start: 0.6811 (mtt-85) cc_final: 0.6169 (mtt-85) REVERT: G 391 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7771 (mtpp) REVERT: G 469 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6904 (mm-30) REVERT: G 609 GLN cc_start: 0.7989 (tp40) cc_final: 0.7402 (tp40) REVERT: G 694 LYS cc_start: 0.8333 (tmtt) cc_final: 0.7866 (tmtt) REVERT: H 156 ASN cc_start: 0.7681 (m-40) cc_final: 0.7478 (m110) REVERT: H 201 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7740 (mtp85) REVERT: H 212 LEU cc_start: 0.8320 (mt) cc_final: 0.8048 (mp) REVERT: H 352 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7499 (mm-30) REVERT: H 484 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7066 (ttp80) REVERT: H 495 ASP cc_start: 0.7923 (t0) cc_final: 0.7605 (t0) REVERT: H 592 PHE cc_start: 0.7747 (t80) cc_final: 0.7320 (t80) REVERT: H 682 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6658 (tptp) outliers start: 57 outliers final: 30 residues processed: 1099 average time/residue: 0.2734 time to fit residues: 457.2121 Evaluate side-chains 1047 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 1012 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 682 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 403 optimal weight: 0.9980 chunk 423 optimal weight: 0.8980 chunk 395 optimal weight: 0.9990 chunk 461 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 292 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 534 HIS A 652 ASN B 156 ASN B 232 ASN B 583 HIS ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS C 652 ASN D 156 ASN D 232 ASN D 383 ASN D 583 HIS E 156 ASN E 383 ASN E 534 HIS F 156 ASN F 652 ASN G 156 ASN G 522 GLN G 534 HIS G 652 ASN H 156 ASN H 232 ASN H 522 GLN H 652 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128561 restraints weight = 56511.295| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.45 r_work: 0.3529 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37552 Z= 0.154 Angle : 0.640 9.249 50728 Z= 0.318 Chirality : 0.042 0.191 5848 Planarity : 0.005 0.050 6536 Dihedral : 4.503 24.337 5128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.01 % Allowed : 14.97 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.13), residues: 4624 helix: 0.39 (0.10), residues: 3168 sheet: -2.91 (0.35), residues: 160 loop : -1.88 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 289 TYR 0.018 0.001 TYR B 568 PHE 0.018 0.002 PHE D 96 TRP 0.010 0.001 TRP F 214 HIS 0.010 0.001 HIS F 587 Details of bonding type rmsd covalent geometry : bond 0.00346 (37552) covalent geometry : angle 0.63951 (50728) hydrogen bonds : bond 0.05156 ( 1882) hydrogen bonds : angle 4.48982 ( 5574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1077 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: A 101 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: A 195 SER cc_start: 0.7965 (m) cc_final: 0.7501 (t) REVERT: A 196 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 197 GLU cc_start: 0.7247 (mp0) cc_final: 0.6960 (mp0) REVERT: A 484 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7667 (mmm-85) REVERT: A 520 GLU cc_start: 0.7457 (tp30) cc_final: 0.7110 (tp30) REVERT: A 592 PHE cc_start: 0.7572 (t80) cc_final: 0.7356 (t80) REVERT: A 609 GLN cc_start: 0.8322 (tp40) cc_final: 0.7664 (tp40) REVERT: A 682 LYS cc_start: 0.6960 (tptp) cc_final: 0.6700 (tptp) REVERT: A 694 LYS cc_start: 0.8432 (tmtt) cc_final: 0.7878 (tptp) REVERT: A 695 ILE cc_start: 0.8733 (pt) cc_final: 0.8476 (pt) REVERT: B 100 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: B 156 ASN cc_start: 0.7703 (m110) cc_final: 0.7436 (m110) REVERT: B 197 GLU cc_start: 0.7394 (mp0) cc_final: 0.7042 (mp0) REVERT: B 200 GLN cc_start: 0.8326 (tt0) cc_final: 0.7693 (mt0) REVERT: B 282 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: B 352 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 363 LYS cc_start: 0.7568 (mppt) cc_final: 0.6989 (mppt) REVERT: B 392 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8206 (ttp-170) REVERT: B 454 ASP cc_start: 0.7823 (m-30) cc_final: 0.7527 (m-30) REVERT: B 459 SER cc_start: 0.8516 (t) cc_final: 0.8221 (p) REVERT: B 497 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7486 (ptp-170) REVERT: B 520 GLU cc_start: 0.7339 (tp30) cc_final: 0.6875 (tp30) REVERT: B 540 THR cc_start: 0.8663 (t) cc_final: 0.8391 (t) REVERT: B 694 LYS cc_start: 0.8255 (tmtt) cc_final: 0.8002 (tptt) REVERT: C 100 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: C 195 SER cc_start: 0.7873 (m) cc_final: 0.7365 (t) REVERT: C 197 GLU cc_start: 0.7275 (mp0) cc_final: 0.6894 (mp0) REVERT: C 286 GLU cc_start: 0.7348 (tp30) cc_final: 0.7063 (tp30) REVERT: C 326 ASP cc_start: 0.7530 (m-30) cc_final: 0.7290 (t0) REVERT: C 380 TYR cc_start: 0.8218 (m-80) cc_final: 0.7995 (m-80) REVERT: C 413 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7544 (mtpp) REVERT: C 483 ASP cc_start: 0.8268 (t0) cc_final: 0.7935 (t70) REVERT: C 682 LYS cc_start: 0.7228 (tptp) cc_final: 0.6930 (tptp) REVERT: C 686 GLU cc_start: 0.7682 (pp20) cc_final: 0.7366 (pp20) REVERT: C 694 LYS cc_start: 0.7999 (tmtt) cc_final: 0.7580 (tmtt) REVERT: D 101 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: D 156 ASN cc_start: 0.7816 (m110) cc_final: 0.7462 (m-40) REVERT: D 157 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7861 (mtm110) REVERT: D 195 SER cc_start: 0.7932 (m) cc_final: 0.7540 (t) REVERT: D 196 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6709 (tm-30) REVERT: D 197 GLU cc_start: 0.7300 (mp0) cc_final: 0.6841 (mp0) REVERT: D 209 ASP cc_start: 0.8073 (t0) cc_final: 0.7841 (t0) REVERT: D 213 TYR cc_start: 0.7959 (t80) cc_final: 0.7615 (t80) REVERT: D 282 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: D 286 GLU cc_start: 0.7259 (tp30) cc_final: 0.6907 (tp30) REVERT: D 289 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7513 (mtm-85) REVERT: D 340 GLU cc_start: 0.7773 (mp0) cc_final: 0.7514 (mp0) REVERT: D 352 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7664 (mm-30) REVERT: D 392 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.8166 (ttp-170) REVERT: D 395 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7701 (ttp-110) REVERT: D 416 GLU cc_start: 0.6527 (mp0) cc_final: 0.6268 (mp0) REVERT: D 454 ASP cc_start: 0.7879 (m-30) cc_final: 0.7565 (m-30) REVERT: D 497 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7287 (ptp-170) REVERT: D 565 PHE cc_start: 0.7921 (t80) cc_final: 0.7607 (t80) REVERT: D 609 GLN cc_start: 0.8333 (tp40) cc_final: 0.7891 (tp40) REVERT: D 682 LYS cc_start: 0.7025 (tptp) cc_final: 0.6655 (tptp) REVERT: D 694 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7632 (tptt) REVERT: D 695 ILE cc_start: 0.8427 (pt) cc_final: 0.8137 (pt) REVERT: E 100 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: E 157 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.8044 (ttm110) REVERT: E 189 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7314 (tm-30) REVERT: E 196 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6778 (tm-30) REVERT: E 349 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7974 (mp) REVERT: E 403 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7221 (ttt-90) REVERT: E 484 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7284 (mtp85) REVERT: E 522 GLN cc_start: 0.8312 (mt0) cc_final: 0.8068 (mt0) REVERT: E 544 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6976 (tm-30) REVERT: E 609 GLN cc_start: 0.8415 (tp40) cc_final: 0.8106 (tp40) REVERT: E 694 LYS cc_start: 0.8405 (tmtt) cc_final: 0.7959 (tmtt) REVERT: F 156 ASN cc_start: 0.7559 (m110) cc_final: 0.7243 (m110) REVERT: F 196 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7056 (tm-30) REVERT: F 197 GLU cc_start: 0.7360 (mp0) cc_final: 0.7028 (mp0) REVERT: F 201 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7768 (mtp85) REVERT: F 209 ASP cc_start: 0.7860 (t0) cc_final: 0.7602 (t0) REVERT: F 212 LEU cc_start: 0.8354 (mt) cc_final: 0.8104 (mp) REVERT: F 232 ASN cc_start: 0.8231 (m-40) cc_final: 0.8017 (m110) REVERT: F 282 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: F 352 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 450 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6478 (mt-10) REVERT: F 454 ASP cc_start: 0.7867 (m-30) cc_final: 0.7488 (m-30) REVERT: F 484 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7086 (ttp80) REVERT: F 540 THR cc_start: 0.8568 (t) cc_final: 0.8265 (t) REVERT: F 592 PHE cc_start: 0.7788 (t80) cc_final: 0.7539 (t80) REVERT: F 609 GLN cc_start: 0.8148 (tp40) cc_final: 0.7514 (tp40) REVERT: F 612 MET cc_start: 0.7777 (tpp) cc_final: 0.7132 (tpp) REVERT: F 694 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7869 (tptp) REVERT: G 155 GLU cc_start: 0.7360 (mp0) cc_final: 0.7093 (mp0) REVERT: G 157 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8070 (ttm110) REVERT: G 189 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7945 (tm-30) REVERT: G 195 SER cc_start: 0.7871 (m) cc_final: 0.7459 (t) REVERT: G 197 GLU cc_start: 0.7172 (mp0) cc_final: 0.6826 (mp0) REVERT: G 244 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7638 (ttm-80) REVERT: G 340 GLU cc_start: 0.7842 (mp0) cc_final: 0.7263 (mp0) REVERT: G 376 ARG cc_start: 0.6961 (mtt-85) cc_final: 0.6653 (mtt-85) REVERT: G 609 GLN cc_start: 0.8099 (tp40) cc_final: 0.7465 (tp40) REVERT: G 681 ILE cc_start: 0.7383 (mp) cc_final: 0.7173 (mp) REVERT: G 694 LYS cc_start: 0.8427 (tmtt) cc_final: 0.7897 (tmtt) REVERT: H 156 ASN cc_start: 0.7668 (m110) cc_final: 0.7401 (m110) REVERT: H 200 GLN cc_start: 0.8259 (tt0) cc_final: 0.7919 (mt0) REVERT: H 201 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7816 (mtp85) REVERT: H 209 ASP cc_start: 0.7861 (t0) cc_final: 0.7550 (t0) REVERT: H 352 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7561 (mm-30) REVERT: H 430 CYS cc_start: 0.7850 (t) cc_final: 0.7599 (t) REVERT: H 458 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7822 (mmpt) REVERT: H 495 ASP cc_start: 0.7984 (t0) cc_final: 0.7644 (t70) REVERT: H 540 THR cc_start: 0.8599 (m) cc_final: 0.8191 (t) REVERT: H 544 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7237 (tm-30) REVERT: H 592 PHE cc_start: 0.7760 (t80) cc_final: 0.7191 (t80) REVERT: H 682 LYS cc_start: 0.7170 (tptp) cc_final: 0.6713 (tptp) outliers start: 118 outliers final: 68 residues processed: 1143 average time/residue: 0.2505 time to fit residues: 436.0383 Evaluate side-chains 1074 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 996 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 612 MET Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 300 optimal weight: 0.6980 chunk 394 optimal weight: 0.6980 chunk 292 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 379 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 466 optimal weight: 0.5980 chunk 383 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 232 ASN D 422 GLN D 522 GLN D 585 GLN D 685 HIS E 418 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128468 restraints weight = 56405.409| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.41 r_work: 0.3532 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37552 Z= 0.143 Angle : 0.632 13.550 50728 Z= 0.310 Chirality : 0.042 0.238 5848 Planarity : 0.004 0.073 6536 Dihedral : 4.405 22.585 5128 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.42 % Allowed : 17.19 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4624 helix: 0.50 (0.10), residues: 3144 sheet: -2.70 (0.37), residues: 160 loop : -1.77 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 146 TYR 0.020 0.001 TYR A 380 PHE 0.023 0.001 PHE A 565 TRP 0.010 0.001 TRP E 638 HIS 0.020 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00322 (37552) covalent geometry : angle 0.63241 (50728) hydrogen bonds : bond 0.04695 ( 1882) hydrogen bonds : angle 4.29203 ( 5574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1045 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.6715 (t80) cc_final: 0.6036 (t80) REVERT: A 157 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8089 (ttm110) REVERT: A 195 SER cc_start: 0.8013 (m) cc_final: 0.7565 (t) REVERT: A 196 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 197 GLU cc_start: 0.7290 (mp0) cc_final: 0.6982 (mp0) REVERT: A 481 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 484 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7534 (mmm-85) REVERT: A 520 GLU cc_start: 0.7473 (tp30) cc_final: 0.7110 (tp30) REVERT: A 544 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 592 PHE cc_start: 0.7573 (t80) cc_final: 0.7258 (t80) REVERT: A 609 GLN cc_start: 0.8279 (tp40) cc_final: 0.7620 (tp40) REVERT: A 682 LYS cc_start: 0.6903 (tptp) cc_final: 0.6648 (tptp) REVERT: A 694 LYS cc_start: 0.8383 (tmtt) cc_final: 0.7836 (tptp) REVERT: A 695 ILE cc_start: 0.8781 (pt) cc_final: 0.8520 (pt) REVERT: B 100 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: B 156 ASN cc_start: 0.7625 (m110) cc_final: 0.7340 (m110) REVERT: B 197 GLU cc_start: 0.7353 (mp0) cc_final: 0.7005 (mp0) REVERT: B 200 GLN cc_start: 0.8326 (tt0) cc_final: 0.7677 (mt0) REVERT: B 282 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: B 326 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7261 (t0) REVERT: B 352 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 363 LYS cc_start: 0.7483 (mppt) cc_final: 0.6943 (mppt) REVERT: B 392 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8177 (ttp-170) REVERT: B 416 GLU cc_start: 0.6810 (mp0) cc_final: 0.6554 (mp0) REVERT: B 454 ASP cc_start: 0.7791 (m-30) cc_final: 0.7483 (m-30) REVERT: B 459 SER cc_start: 0.8460 (t) cc_final: 0.8215 (p) REVERT: B 485 SER cc_start: 0.8191 (t) cc_final: 0.7715 (t) REVERT: B 497 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7484 (ptp-170) REVERT: B 520 GLU cc_start: 0.7309 (tp30) cc_final: 0.6880 (tp30) REVERT: B 540 THR cc_start: 0.8683 (t) cc_final: 0.8400 (t) REVERT: B 694 LYS cc_start: 0.8301 (tmtt) cc_final: 0.7913 (tptp) REVERT: C 100 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: C 149 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 173 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8095 (mtmm) REVERT: C 195 SER cc_start: 0.8005 (m) cc_final: 0.7500 (t) REVERT: C 197 GLU cc_start: 0.7246 (mp0) cc_final: 0.6842 (mp0) REVERT: C 248 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8328 (mttp) REVERT: C 286 GLU cc_start: 0.7355 (tp30) cc_final: 0.7083 (tp30) REVERT: C 380 TYR cc_start: 0.8239 (m-80) cc_final: 0.8018 (m-80) REVERT: C 682 LYS cc_start: 0.7209 (tptp) cc_final: 0.6920 (tptp) REVERT: C 686 GLU cc_start: 0.7674 (pp20) cc_final: 0.7367 (pp20) REVERT: C 694 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7604 (tptt) REVERT: D 143 GLN cc_start: 0.7031 (mp10) cc_final: 0.6808 (mp10) REVERT: D 156 ASN cc_start: 0.7774 (m110) cc_final: 0.7473 (m-40) REVERT: D 157 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7586 (mtm180) REVERT: D 195 SER cc_start: 0.7981 (m) cc_final: 0.7599 (t) REVERT: D 196 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6823 (tm-30) REVERT: D 197 GLU cc_start: 0.7315 (mp0) cc_final: 0.6872 (mp0) REVERT: D 209 ASP cc_start: 0.8065 (t0) cc_final: 0.7796 (t0) REVERT: D 213 TYR cc_start: 0.8063 (t80) cc_final: 0.7689 (t80) REVERT: D 248 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8227 (mttp) REVERT: D 282 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: D 340 GLU cc_start: 0.7746 (mp0) cc_final: 0.7491 (mp0) REVERT: D 352 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 395 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7661 (ttp-110) REVERT: D 416 GLU cc_start: 0.6575 (mp0) cc_final: 0.6293 (mp0) REVERT: D 448 GLU cc_start: 0.7500 (tt0) cc_final: 0.7269 (tt0) REVERT: D 454 ASP cc_start: 0.7826 (m-30) cc_final: 0.7482 (m-30) REVERT: D 497 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7318 (ptp-170) REVERT: D 609 GLN cc_start: 0.8282 (tp40) cc_final: 0.7852 (tp40) REVERT: D 694 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7664 (tptt) REVERT: D 695 ILE cc_start: 0.8479 (pt) cc_final: 0.8156 (pt) REVERT: E 149 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7304 (mm-30) REVERT: E 157 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8043 (ttm110) REVERT: E 189 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7348 (tm-30) REVERT: E 196 GLU cc_start: 0.7190 (tm-30) cc_final: 0.5920 (tm-30) REVERT: E 200 GLN cc_start: 0.8389 (tt0) cc_final: 0.7639 (mt0) REVERT: E 349 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8016 (mp) REVERT: E 485 SER cc_start: 0.7899 (t) cc_final: 0.7439 (t) REVERT: E 522 GLN cc_start: 0.8351 (mt0) cc_final: 0.8149 (mt0) REVERT: E 544 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7089 (tm-30) REVERT: E 609 GLN cc_start: 0.8425 (tp40) cc_final: 0.8128 (tp40) REVERT: E 694 LYS cc_start: 0.8415 (tmtt) cc_final: 0.7931 (tmtt) REVERT: F 156 ASN cc_start: 0.7468 (m110) cc_final: 0.7150 (m110) REVERT: F 197 GLU cc_start: 0.7371 (mp0) cc_final: 0.7036 (mp0) REVERT: F 201 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7753 (mtp85) REVERT: F 209 ASP cc_start: 0.7835 (t0) cc_final: 0.7555 (t0) REVERT: F 212 LEU cc_start: 0.8268 (mt) cc_final: 0.7918 (mp) REVERT: F 215 CYS cc_start: 0.7444 (m) cc_final: 0.7141 (m) REVERT: F 232 ASN cc_start: 0.8267 (m-40) cc_final: 0.8055 (m-40) REVERT: F 352 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7653 (mm-30) REVERT: F 454 ASP cc_start: 0.7838 (m-30) cc_final: 0.7483 (m-30) REVERT: F 484 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7191 (ttp80) REVERT: F 540 THR cc_start: 0.8636 (t) cc_final: 0.8336 (t) REVERT: F 592 PHE cc_start: 0.7750 (t80) cc_final: 0.7541 (t80) REVERT: F 609 GLN cc_start: 0.8075 (tp40) cc_final: 0.7461 (tp40) REVERT: F 612 MET cc_start: 0.7687 (tpp) cc_final: 0.7018 (tpp) REVERT: F 638 TRP cc_start: 0.7202 (m-90) cc_final: 0.6863 (m-90) REVERT: F 694 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7894 (tptp) REVERT: G 100 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: G 155 GLU cc_start: 0.7329 (mp0) cc_final: 0.7048 (mp0) REVERT: G 157 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8079 (ttm110) REVERT: G 189 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 195 SER cc_start: 0.8001 (m) cc_final: 0.7642 (t) REVERT: G 196 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6561 (tm-30) REVERT: G 197 GLU cc_start: 0.7191 (mp0) cc_final: 0.6895 (mp0) REVERT: G 200 GLN cc_start: 0.8310 (tt0) cc_final: 0.7962 (mt0) REVERT: G 244 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7664 (ttm-80) REVERT: G 271 CYS cc_start: 0.7131 (m) cc_final: 0.6861 (m) REVERT: G 349 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7974 (mp) REVERT: G 376 ARG cc_start: 0.7020 (mtt-85) cc_final: 0.6728 (mtt180) REVERT: G 520 GLU cc_start: 0.7492 (tp30) cc_final: 0.7262 (tp30) REVERT: G 694 LYS cc_start: 0.8413 (tmtt) cc_final: 0.7869 (tmtt) REVERT: H 101 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: H 143 GLN cc_start: 0.7126 (mp10) cc_final: 0.6865 (mp10) REVERT: H 149 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7213 (mm-30) REVERT: H 156 ASN cc_start: 0.7567 (m110) cc_final: 0.7279 (m110) REVERT: H 201 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7831 (mtp85) REVERT: H 209 ASP cc_start: 0.7896 (t0) cc_final: 0.7567 (t0) REVERT: H 282 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: H 352 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7702 (mm-30) REVERT: H 458 LYS cc_start: 0.8024 (mmpt) cc_final: 0.7807 (mmpt) REVERT: H 485 SER cc_start: 0.8263 (t) cc_final: 0.7825 (t) REVERT: H 495 ASP cc_start: 0.7922 (t0) cc_final: 0.7658 (t0) REVERT: H 540 THR cc_start: 0.8603 (m) cc_final: 0.8130 (t) REVERT: H 544 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7308 (tm-30) REVERT: H 609 GLN cc_start: 0.7922 (tp40) cc_final: 0.7314 (tp40) REVERT: H 682 LYS cc_start: 0.7197 (tptp) cc_final: 0.6889 (tptp) REVERT: H 694 LYS cc_start: 0.8406 (tptt) cc_final: 0.8190 (tptp) outliers start: 134 outliers final: 70 residues processed: 1118 average time/residue: 0.2710 time to fit residues: 461.5338 Evaluate side-chains 1076 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 995 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 302 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 442 optimal weight: 0.8980 chunk 378 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN D 422 GLN D 522 GLN D 585 GLN ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 437 GLN F 522 GLN G 522 GLN H 423 GLN H 522 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128433 restraints weight = 56361.995| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.41 r_work: 0.3523 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37552 Z= 0.140 Angle : 0.620 11.517 50728 Z= 0.304 Chirality : 0.041 0.226 5848 Planarity : 0.004 0.062 6536 Dihedral : 4.366 24.172 5128 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.75 % Allowed : 17.83 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.13), residues: 4624 helix: 0.59 (0.10), residues: 3144 sheet: -2.60 (0.37), residues: 160 loop : -1.76 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 146 TYR 0.020 0.001 TYR A 380 PHE 0.018 0.001 PHE H 592 TRP 0.008 0.001 TRP E 638 HIS 0.027 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00318 (37552) covalent geometry : angle 0.61982 (50728) hydrogen bonds : bond 0.04524 ( 1882) hydrogen bonds : angle 4.17738 ( 5574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1044 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7214 (mp0) cc_final: 0.6925 (mp0) REVERT: A 157 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8120 (ttm110) REVERT: A 195 SER cc_start: 0.7973 (m) cc_final: 0.7561 (t) REVERT: A 196 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 197 GLU cc_start: 0.7244 (mp0) cc_final: 0.6970 (mp0) REVERT: A 209 ASP cc_start: 0.8072 (t0) cc_final: 0.7697 (t0) REVERT: A 479 TYR cc_start: 0.8172 (m-80) cc_final: 0.7861 (m-80) REVERT: A 484 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7553 (mmm-85) REVERT: A 485 SER cc_start: 0.8194 (t) cc_final: 0.7717 (t) REVERT: A 520 GLU cc_start: 0.7506 (tp30) cc_final: 0.7128 (tp30) REVERT: A 592 PHE cc_start: 0.7585 (t80) cc_final: 0.7266 (t80) REVERT: A 609 GLN cc_start: 0.8299 (tp40) cc_final: 0.7637 (tp40) REVERT: A 682 LYS cc_start: 0.7010 (tptp) cc_final: 0.6640 (tptp) REVERT: A 694 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7791 (tptp) REVERT: A 695 ILE cc_start: 0.8763 (pt) cc_final: 0.8508 (pt) REVERT: B 94 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: B 100 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: B 156 ASN cc_start: 0.7629 (m110) cc_final: 0.7313 (m110) REVERT: B 189 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 197 GLU cc_start: 0.7389 (mp0) cc_final: 0.7051 (mp0) REVERT: B 200 GLN cc_start: 0.8369 (tt0) cc_final: 0.7717 (mt0) REVERT: B 282 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: B 326 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7284 (t0) REVERT: B 352 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 363 LYS cc_start: 0.7446 (mppt) cc_final: 0.6937 (mppt) REVERT: B 416 GLU cc_start: 0.6768 (mp0) cc_final: 0.6450 (mp0) REVERT: B 451 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7879 (mt) REVERT: B 454 ASP cc_start: 0.7769 (m-30) cc_final: 0.7470 (m-30) REVERT: B 459 SER cc_start: 0.8517 (t) cc_final: 0.8270 (p) REVERT: B 484 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7272 (ttp80) REVERT: B 485 SER cc_start: 0.8225 (t) cc_final: 0.7649 (t) REVERT: B 497 ARG cc_start: 0.7833 (mtm180) cc_final: 0.7457 (ptp-170) REVERT: B 520 GLU cc_start: 0.7348 (tp30) cc_final: 0.6886 (tp30) REVERT: B 540 THR cc_start: 0.8639 (t) cc_final: 0.8361 (t) REVERT: B 694 LYS cc_start: 0.8373 (tmtt) cc_final: 0.7988 (tptp) REVERT: C 100 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: C 149 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 173 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7633 (mtmm) REVERT: C 195 SER cc_start: 0.7988 (m) cc_final: 0.7490 (t) REVERT: C 197 GLU cc_start: 0.7187 (mp0) cc_final: 0.6886 (mp0) REVERT: C 248 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8316 (mttp) REVERT: C 286 GLU cc_start: 0.7381 (tp30) cc_final: 0.7117 (tp30) REVERT: C 481 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 484 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7898 (mmm-85) REVERT: C 682 LYS cc_start: 0.7222 (tptp) cc_final: 0.6929 (tptp) REVERT: C 686 GLU cc_start: 0.7690 (pp20) cc_final: 0.7386 (pp20) REVERT: C 694 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7584 (tptt) REVERT: D 101 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: D 156 ASN cc_start: 0.7789 (m110) cc_final: 0.7502 (m110) REVERT: D 157 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7800 (mtm-85) REVERT: D 195 SER cc_start: 0.7996 (m) cc_final: 0.7610 (t) REVERT: D 196 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6856 (tm-30) REVERT: D 197 GLU cc_start: 0.7354 (mp0) cc_final: 0.6918 (mp0) REVERT: D 209 ASP cc_start: 0.8042 (t0) cc_final: 0.7735 (t0) REVERT: D 213 TYR cc_start: 0.8078 (t80) cc_final: 0.7725 (t80) REVERT: D 248 LYS cc_start: 0.8566 (mmtp) cc_final: 0.8199 (mttp) REVERT: D 282 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: D 352 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 392 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8190 (ttp-170) REVERT: D 395 ARG cc_start: 0.7914 (ptp-110) cc_final: 0.7650 (ttp-110) REVERT: D 416 GLU cc_start: 0.6606 (mp0) cc_final: 0.6332 (mp0) REVERT: D 444 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8599 (mt) REVERT: D 448 GLU cc_start: 0.7541 (tt0) cc_final: 0.7290 (tt0) REVERT: D 485 SER cc_start: 0.8171 (t) cc_final: 0.7680 (t) REVERT: D 495 ASP cc_start: 0.7786 (t0) cc_final: 0.7567 (t0) REVERT: D 497 ARG cc_start: 0.7690 (mtm180) cc_final: 0.7279 (ptp-170) REVERT: D 540 THR cc_start: 0.8678 (t) cc_final: 0.8454 (t) REVERT: D 609 GLN cc_start: 0.8278 (tp40) cc_final: 0.7847 (tp40) REVERT: D 694 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7634 (tptt) REVERT: D 695 ILE cc_start: 0.8471 (pt) cc_final: 0.8165 (pt) REVERT: E 96 PHE cc_start: 0.6702 (t80) cc_final: 0.6006 (t80) REVERT: E 157 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8049 (ttm110) REVERT: E 196 GLU cc_start: 0.7224 (tm-30) cc_final: 0.5912 (tm-30) REVERT: E 197 GLU cc_start: 0.7157 (mp0) cc_final: 0.6939 (mp0) REVERT: E 200 GLN cc_start: 0.8386 (tt0) cc_final: 0.7607 (mt0) REVERT: E 349 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8025 (mp) REVERT: E 403 ARG cc_start: 0.7676 (ttt-90) cc_final: 0.7405 (ttt-90) REVERT: E 448 GLU cc_start: 0.7534 (tt0) cc_final: 0.7301 (tt0) REVERT: E 485 SER cc_start: 0.7891 (t) cc_final: 0.7441 (t) REVERT: E 544 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7175 (tm-30) REVERT: E 586 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8048 (mm) REVERT: E 694 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7926 (tmtt) REVERT: F 156 ASN cc_start: 0.7475 (m110) cc_final: 0.7157 (m110) REVERT: F 197 GLU cc_start: 0.7369 (mp0) cc_final: 0.7031 (mp0) REVERT: F 201 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7719 (mtp85) REVERT: F 209 ASP cc_start: 0.7905 (t0) cc_final: 0.7558 (t0) REVERT: F 212 LEU cc_start: 0.8269 (mt) cc_final: 0.7905 (mp) REVERT: F 215 CYS cc_start: 0.7423 (m) cc_final: 0.7125 (m) REVERT: F 232 ASN cc_start: 0.8272 (m-40) cc_final: 0.8052 (m-40) REVERT: F 249 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7820 (mmm-85) REVERT: F 352 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7701 (mm-30) REVERT: F 444 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (mt) REVERT: F 448 GLU cc_start: 0.7572 (tt0) cc_final: 0.7356 (tt0) REVERT: F 454 ASP cc_start: 0.7828 (m-30) cc_final: 0.7463 (m-30) REVERT: F 484 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7146 (ttp80) REVERT: F 540 THR cc_start: 0.8673 (t) cc_final: 0.8387 (t) REVERT: F 544 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7344 (tm-30) REVERT: F 592 PHE cc_start: 0.7748 (t80) cc_final: 0.7503 (t80) REVERT: F 609 GLN cc_start: 0.8124 (tp40) cc_final: 0.7511 (tp40) REVERT: F 612 MET cc_start: 0.7744 (tpp) cc_final: 0.7032 (tpp) REVERT: F 638 TRP cc_start: 0.7233 (m-90) cc_final: 0.6889 (m-90) REVERT: F 694 LYS cc_start: 0.8329 (tmtt) cc_final: 0.7921 (tptp) REVERT: G 100 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: G 155 GLU cc_start: 0.7317 (mp0) cc_final: 0.7034 (mp0) REVERT: G 157 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8011 (ttm110) REVERT: G 189 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7998 (tm-30) REVERT: G 195 SER cc_start: 0.8025 (m) cc_final: 0.7639 (t) REVERT: G 196 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6640 (tm-30) REVERT: G 197 GLU cc_start: 0.7214 (mp0) cc_final: 0.6957 (mp0) REVERT: G 200 GLN cc_start: 0.8311 (tt0) cc_final: 0.8051 (mt0) REVERT: G 349 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8051 (mp) REVERT: G 376 ARG cc_start: 0.7020 (mtt-85) cc_final: 0.6722 (mtt-85) REVERT: G 520 GLU cc_start: 0.7500 (tp30) cc_final: 0.7239 (tp30) REVERT: G 694 LYS cc_start: 0.8410 (tmtt) cc_final: 0.7851 (tmtt) REVERT: H 143 GLN cc_start: 0.7108 (mp10) cc_final: 0.6862 (mp10) REVERT: H 156 ASN cc_start: 0.7593 (m110) cc_final: 0.7270 (m110) REVERT: H 189 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7970 (tm-30) REVERT: H 201 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7830 (mtp85) REVERT: H 209 ASP cc_start: 0.7982 (t0) cc_final: 0.7592 (t0) REVERT: H 247 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 282 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: H 286 GLU cc_start: 0.7344 (tp30) cc_final: 0.7107 (tp30) REVERT: H 352 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7700 (mm-30) REVERT: H 363 LYS cc_start: 0.7540 (mppt) cc_final: 0.7048 (mppt) REVERT: H 430 CYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7751 (t) REVERT: H 450 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6507 (mt-10) REVERT: H 454 ASP cc_start: 0.7869 (m-30) cc_final: 0.7509 (m-30) REVERT: H 458 LYS cc_start: 0.8045 (mmpt) cc_final: 0.7844 (mmpt) REVERT: H 540 THR cc_start: 0.8584 (m) cc_final: 0.8103 (t) REVERT: H 544 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7346 (tm-30) REVERT: H 609 GLN cc_start: 0.7929 (tp40) cc_final: 0.7317 (tp40) REVERT: H 682 LYS cc_start: 0.7195 (tptp) cc_final: 0.6870 (tptp) REVERT: H 693 GLU cc_start: 0.7518 (tp30) cc_final: 0.7196 (tp30) REVERT: H 694 LYS cc_start: 0.8472 (tptt) cc_final: 0.8235 (tptt) outliers start: 147 outliers final: 92 residues processed: 1118 average time/residue: 0.2455 time to fit residues: 420.1541 Evaluate side-chains 1114 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1005 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 612 MET Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 400 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 406 optimal weight: 0.5980 chunk 459 optimal weight: 1.9990 chunk 243 optimal weight: 0.0070 chunk 112 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 128 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS C 418 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN F 422 GLN F 522 GLN F 585 GLN G 422 GLN G 522 GLN G 585 GLN H 422 GLN H 522 GLN H 587 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127909 restraints weight = 56396.674| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.41 r_work: 0.3515 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37552 Z= 0.141 Angle : 0.624 15.913 50728 Z= 0.305 Chirality : 0.041 0.174 5848 Planarity : 0.004 0.049 6536 Dihedral : 4.321 23.708 5128 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.03 % Allowed : 18.16 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4624 helix: 0.62 (0.10), residues: 3144 sheet: -2.45 (0.38), residues: 160 loop : -1.73 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 146 TYR 0.019 0.001 TYR A 380 PHE 0.015 0.001 PHE A 565 TRP 0.008 0.001 TRP A 638 HIS 0.008 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00321 (37552) covalent geometry : angle 0.62386 (50728) hydrogen bonds : bond 0.04418 ( 1882) hydrogen bonds : angle 4.12069 ( 5574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1076 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8131 (ttm110) REVERT: A 195 SER cc_start: 0.7993 (m) cc_final: 0.7577 (t) REVERT: A 196 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 197 GLU cc_start: 0.7269 (mp0) cc_final: 0.7051 (mp0) REVERT: A 253 TRP cc_start: 0.8325 (m100) cc_final: 0.8072 (m100) REVERT: A 289 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7551 (mmt90) REVERT: A 376 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6854 (mtm-85) REVERT: A 479 TYR cc_start: 0.8149 (m-80) cc_final: 0.7832 (m-80) REVERT: A 484 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7559 (mmm-85) REVERT: A 485 SER cc_start: 0.8183 (t) cc_final: 0.7701 (t) REVERT: A 592 PHE cc_start: 0.7605 (t80) cc_final: 0.7338 (t80) REVERT: A 609 GLN cc_start: 0.8312 (tp40) cc_final: 0.7650 (tp40) REVERT: A 682 LYS cc_start: 0.7015 (tptp) cc_final: 0.6628 (tptp) REVERT: A 694 LYS cc_start: 0.8340 (tmtt) cc_final: 0.7776 (tptp) REVERT: A 695 ILE cc_start: 0.8751 (pt) cc_final: 0.8475 (pt) REVERT: B 100 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 156 ASN cc_start: 0.7640 (m110) cc_final: 0.7305 (m110) REVERT: B 189 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 196 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6151 (tm-30) REVERT: B 197 GLU cc_start: 0.7377 (mp0) cc_final: 0.7068 (mp0) REVERT: B 200 GLN cc_start: 0.8376 (tt0) cc_final: 0.7513 (mt0) REVERT: B 252 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 282 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: B 326 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7282 (t0) REVERT: B 352 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 363 LYS cc_start: 0.7510 (mppt) cc_final: 0.6999 (mppt) REVERT: B 376 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7483 (ttm-80) REVERT: B 392 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.8234 (ttp-170) REVERT: B 416 GLU cc_start: 0.6793 (mp0) cc_final: 0.6513 (mp0) REVERT: B 444 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 451 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7887 (mt) REVERT: B 454 ASP cc_start: 0.7721 (m-30) cc_final: 0.7424 (m-30) REVERT: B 459 SER cc_start: 0.8507 (t) cc_final: 0.8260 (p) REVERT: B 484 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7304 (ttp80) REVERT: B 485 SER cc_start: 0.8252 (t) cc_final: 0.7671 (t) REVERT: B 497 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7448 (ptp-170) REVERT: B 540 THR cc_start: 0.8636 (t) cc_final: 0.8359 (t) REVERT: B 694 LYS cc_start: 0.8420 (tmtt) cc_final: 0.8039 (tptp) REVERT: C 100 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: C 149 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7281 (mm-30) REVERT: C 173 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8254 (mtmm) REVERT: C 195 SER cc_start: 0.8033 (m) cc_final: 0.7546 (t) REVERT: C 196 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6777 (tm-30) REVERT: C 197 GLU cc_start: 0.7225 (mp0) cc_final: 0.6982 (mp0) REVERT: C 248 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8295 (mttp) REVERT: C 286 GLU cc_start: 0.7421 (tp30) cc_final: 0.7172 (tp30) REVERT: C 392 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7980 (ttp-110) REVERT: C 481 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (p) REVERT: C 483 ASP cc_start: 0.8160 (t0) cc_final: 0.7949 (t0) REVERT: C 484 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7861 (mmm-85) REVERT: C 694 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7613 (tptt) REVERT: D 156 ASN cc_start: 0.7766 (m110) cc_final: 0.7471 (m110) REVERT: D 157 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7768 (mtm-85) REVERT: D 195 SER cc_start: 0.8013 (m) cc_final: 0.7610 (t) REVERT: D 196 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6870 (tm-30) REVERT: D 197 GLU cc_start: 0.7370 (mp0) cc_final: 0.6907 (mp0) REVERT: D 209 ASP cc_start: 0.8086 (t0) cc_final: 0.7768 (t0) REVERT: D 213 TYR cc_start: 0.8110 (t80) cc_final: 0.7733 (t80) REVERT: D 248 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8152 (mttp) REVERT: D 282 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: D 352 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 392 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.7938 (ttp-170) REVERT: D 395 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7643 (ttp-110) REVERT: D 416 GLU cc_start: 0.6507 (mp0) cc_final: 0.6246 (mp0) REVERT: D 418 GLN cc_start: 0.8443 (mm110) cc_final: 0.8091 (mm-40) REVERT: D 430 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7567 (t) REVERT: D 444 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8600 (mt) REVERT: D 448 GLU cc_start: 0.7559 (tt0) cc_final: 0.7297 (tt0) REVERT: D 485 SER cc_start: 0.8180 (t) cc_final: 0.7696 (t) REVERT: D 540 THR cc_start: 0.8673 (t) cc_final: 0.8439 (t) REVERT: D 609 GLN cc_start: 0.8271 (tp40) cc_final: 0.7851 (tp40) REVERT: D 694 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7659 (tptt) REVERT: D 695 ILE cc_start: 0.8488 (pt) cc_final: 0.8181 (pt) REVERT: E 96 PHE cc_start: 0.7288 (t80) cc_final: 0.7035 (t80) REVERT: E 157 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8080 (ttm110) REVERT: E 196 GLU cc_start: 0.7277 (tm-30) cc_final: 0.5938 (tm-30) REVERT: E 197 GLU cc_start: 0.7174 (mp0) cc_final: 0.6943 (mp0) REVERT: E 200 GLN cc_start: 0.8401 (tt0) cc_final: 0.7594 (mt0) REVERT: E 247 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7270 (tm-30) REVERT: E 403 ARG cc_start: 0.7663 (ttt-90) cc_final: 0.7378 (ttt-90) REVERT: E 485 SER cc_start: 0.7910 (t) cc_final: 0.7356 (t) REVERT: E 519 SER cc_start: 0.8690 (t) cc_final: 0.8122 (p) REVERT: E 544 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7185 (tm-30) REVERT: E 586 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8117 (mm) REVERT: E 694 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7925 (tmtt) REVERT: F 156 ASN cc_start: 0.7476 (m110) cc_final: 0.7140 (m110) REVERT: F 196 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6861 (tm-30) REVERT: F 197 GLU cc_start: 0.7313 (mp0) cc_final: 0.6995 (mp0) REVERT: F 200 GLN cc_start: 0.8407 (tt0) cc_final: 0.8090 (mt0) REVERT: F 201 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7760 (mtp85) REVERT: F 209 ASP cc_start: 0.7913 (t0) cc_final: 0.7567 (t0) REVERT: F 212 LEU cc_start: 0.8260 (mt) cc_final: 0.8033 (mp) REVERT: F 232 ASN cc_start: 0.8272 (m-40) cc_final: 0.8048 (m-40) REVERT: F 249 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7851 (mmm-85) REVERT: F 352 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7715 (mm-30) REVERT: F 392 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8116 (ttp-110) REVERT: F 444 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8637 (mt) REVERT: F 454 ASP cc_start: 0.7755 (m-30) cc_final: 0.7427 (m-30) REVERT: F 484 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7194 (ttp80) REVERT: F 485 SER cc_start: 0.8128 (t) cc_final: 0.7546 (t) REVERT: F 520 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7279 (tm-30) REVERT: F 540 THR cc_start: 0.8695 (t) cc_final: 0.8412 (t) REVERT: F 544 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7383 (tm-30) REVERT: F 587 HIS cc_start: 0.8339 (m90) cc_final: 0.7969 (m90) REVERT: F 592 PHE cc_start: 0.7741 (t80) cc_final: 0.7520 (t80) REVERT: F 609 GLN cc_start: 0.8116 (tp40) cc_final: 0.7501 (tp40) REVERT: F 612 MET cc_start: 0.7742 (tpp) cc_final: 0.7025 (tpp) REVERT: F 638 TRP cc_start: 0.7262 (m-90) cc_final: 0.6945 (m-90) REVERT: F 694 LYS cc_start: 0.8368 (tmtt) cc_final: 0.7850 (tptp) REVERT: G 100 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: G 157 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7976 (ttm110) REVERT: G 189 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8000 (tm-30) REVERT: G 195 SER cc_start: 0.8031 (m) cc_final: 0.7640 (t) REVERT: G 196 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6188 (tm-30) REVERT: G 197 GLU cc_start: 0.7196 (mp0) cc_final: 0.6952 (mp0) REVERT: G 200 GLN cc_start: 0.8329 (tt0) cc_final: 0.7587 (mt0) REVERT: G 247 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7296 (tm-30) REVERT: G 349 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8062 (mp) REVERT: G 376 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6716 (mtt-85) REVERT: G 521 GLN cc_start: 0.7673 (tp-100) cc_final: 0.7465 (tp-100) REVERT: G 694 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7851 (tmtt) REVERT: H 143 GLN cc_start: 0.7099 (mp10) cc_final: 0.6861 (mp10) REVERT: H 156 ASN cc_start: 0.7576 (m110) cc_final: 0.7259 (m110) REVERT: H 165 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8139 (tp) REVERT: H 196 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7219 (tm-30) REVERT: H 197 GLU cc_start: 0.7429 (mp0) cc_final: 0.7101 (mp0) REVERT: H 201 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7930 (ttp80) REVERT: H 209 ASP cc_start: 0.7990 (t0) cc_final: 0.7598 (t0) REVERT: H 247 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7273 (tm-30) REVERT: H 282 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: H 286 GLU cc_start: 0.7328 (tp30) cc_final: 0.7126 (tp30) REVERT: H 303 LEU cc_start: 0.8437 (mp) cc_final: 0.8208 (mm) REVERT: H 352 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7686 (mm-30) REVERT: H 363 LYS cc_start: 0.7531 (mppt) cc_final: 0.7034 (mppt) REVERT: H 444 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8646 (mt) REVERT: H 450 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6536 (mt-10) REVERT: H 454 ASP cc_start: 0.7850 (m-30) cc_final: 0.7499 (m-30) REVERT: H 540 THR cc_start: 0.8567 (m) cc_final: 0.8081 (t) REVERT: H 544 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7379 (tm-30) REVERT: H 609 GLN cc_start: 0.7937 (tp40) cc_final: 0.7335 (tp40) REVERT: H 682 LYS cc_start: 0.7196 (tptp) cc_final: 0.6823 (tptp) REVERT: H 693 GLU cc_start: 0.7516 (tp30) cc_final: 0.7193 (tp30) REVERT: H 694 LYS cc_start: 0.8458 (tptt) cc_final: 0.8181 (tptt) outliers start: 158 outliers final: 101 residues processed: 1158 average time/residue: 0.2670 time to fit residues: 471.5586 Evaluate side-chains 1134 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1016 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 469 optimal weight: 0.0170 chunk 31 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 457 optimal weight: 0.9990 chunk 358 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 380 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS C 383 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 583 HIS D 585 GLN D 685 HIS E 585 GLN E 652 ASN F 422 GLN F 522 GLN F 585 GLN G 422 GLN G 522 GLN G 585 GLN H 422 GLN H 423 GLN H 522 GLN H 587 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126196 restraints weight = 56671.728| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.41 r_work: 0.3487 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37552 Z= 0.187 Angle : 0.657 13.695 50728 Z= 0.326 Chirality : 0.043 0.172 5848 Planarity : 0.005 0.051 6536 Dihedral : 4.445 23.803 5128 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.75 % Allowed : 19.34 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 4624 helix: 0.47 (0.10), residues: 3144 sheet: -2.36 (0.39), residues: 160 loop : -1.71 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 484 TYR 0.020 0.002 TYR A 380 PHE 0.024 0.002 PHE E 96 TRP 0.010 0.001 TRP A 638 HIS 0.021 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00425 (37552) covalent geometry : angle 0.65725 (50728) hydrogen bonds : bond 0.04867 ( 1882) hydrogen bonds : angle 4.18764 ( 5574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1052 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8137 (ttm110) REVERT: A 195 SER cc_start: 0.8090 (m) cc_final: 0.7681 (t) REVERT: A 196 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6475 (tm-30) REVERT: A 197 GLU cc_start: 0.7274 (mp0) cc_final: 0.6994 (mp0) REVERT: A 200 GLN cc_start: 0.8319 (tt0) cc_final: 0.7993 (mt0) REVERT: A 376 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6822 (mtm-85) REVERT: A 413 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7938 (mmtp) REVERT: A 479 TYR cc_start: 0.8204 (m-80) cc_final: 0.7860 (m-10) REVERT: A 484 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7557 (mmm-85) REVERT: A 485 SER cc_start: 0.8162 (t) cc_final: 0.7667 (t) REVERT: A 520 GLU cc_start: 0.7575 (tp30) cc_final: 0.7127 (tp30) REVERT: A 592 PHE cc_start: 0.7603 (t80) cc_final: 0.7295 (t80) REVERT: A 609 GLN cc_start: 0.8296 (tp40) cc_final: 0.7645 (tp40) REVERT: A 682 LYS cc_start: 0.7036 (tptp) cc_final: 0.6663 (tptp) REVERT: A 694 LYS cc_start: 0.8331 (tmtt) cc_final: 0.7929 (tptp) REVERT: B 100 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 156 ASN cc_start: 0.7650 (m110) cc_final: 0.7313 (m110) REVERT: B 189 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 196 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6196 (tm-30) REVERT: B 197 GLU cc_start: 0.7352 (mp0) cc_final: 0.7064 (mp0) REVERT: B 200 GLN cc_start: 0.8412 (tt0) cc_final: 0.7548 (mt0) REVERT: B 252 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 282 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: B 326 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7248 (t0) REVERT: B 352 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 363 LYS cc_start: 0.7569 (mppt) cc_final: 0.7037 (mppt) REVERT: B 392 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8240 (ttp-170) REVERT: B 416 GLU cc_start: 0.6809 (mp0) cc_final: 0.6531 (mp0) REVERT: B 444 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 451 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7916 (mt) REVERT: B 454 ASP cc_start: 0.7723 (m-30) cc_final: 0.7414 (m-30) REVERT: B 459 SER cc_start: 0.8527 (t) cc_final: 0.8241 (p) REVERT: B 485 SER cc_start: 0.8262 (t) cc_final: 0.7761 (t) REVERT: B 520 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7208 (tp30) REVERT: B 540 THR cc_start: 0.8655 (t) cc_final: 0.8383 (t) REVERT: B 694 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8077 (tptp) REVERT: C 100 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: C 149 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 173 LYS cc_start: 0.8511 (mtmm) cc_final: 0.7683 (mtmm) REVERT: C 195 SER cc_start: 0.8029 (m) cc_final: 0.7568 (t) REVERT: C 196 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6814 (tm-30) REVERT: C 197 GLU cc_start: 0.7229 (mp0) cc_final: 0.6917 (mp0) REVERT: C 247 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 248 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8188 (mttp) REVERT: C 392 ARG cc_start: 0.8425 (ttm170) cc_final: 0.7961 (ttp-110) REVERT: C 413 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7897 (mmtm) REVERT: C 454 ASP cc_start: 0.7847 (m-30) cc_final: 0.7509 (m-30) REVERT: C 483 ASP cc_start: 0.8147 (t0) cc_final: 0.7604 (t70) REVERT: C 694 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7697 (tptt) REVERT: D 149 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7373 (mm-30) REVERT: D 156 ASN cc_start: 0.7743 (m110) cc_final: 0.7370 (m110) REVERT: D 157 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7771 (mtm-85) REVERT: D 195 SER cc_start: 0.8153 (m) cc_final: 0.7726 (t) REVERT: D 196 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6910 (tm-30) REVERT: D 197 GLU cc_start: 0.7392 (mp0) cc_final: 0.6947 (mp0) REVERT: D 209 ASP cc_start: 0.8108 (t0) cc_final: 0.7766 (t0) REVERT: D 248 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8188 (mttp) REVERT: D 282 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: D 304 ASP cc_start: 0.7610 (t0) cc_final: 0.7397 (t0) REVERT: D 352 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 363 LYS cc_start: 0.7606 (mppt) cc_final: 0.7047 (mppt) REVERT: D 383 ASN cc_start: 0.8323 (t0) cc_final: 0.8049 (t0) REVERT: D 395 ARG cc_start: 0.7931 (ptp-110) cc_final: 0.7649 (ttp-110) REVERT: D 416 GLU cc_start: 0.6541 (mp0) cc_final: 0.6306 (mp0) REVERT: D 430 CYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (t) REVERT: D 444 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8599 (mt) REVERT: D 485 SER cc_start: 0.8152 (t) cc_final: 0.7657 (t) REVERT: D 540 THR cc_start: 0.8677 (t) cc_final: 0.8450 (t) REVERT: D 609 GLN cc_start: 0.8242 (tp40) cc_final: 0.7838 (tp40) REVERT: D 694 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7709 (tptt) REVERT: D 695 ILE cc_start: 0.8558 (pt) cc_final: 0.8255 (pt) REVERT: E 157 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8096 (ttm110) REVERT: E 196 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6171 (tm-30) REVERT: E 197 GLU cc_start: 0.7198 (mp0) cc_final: 0.6980 (mp0) REVERT: E 200 GLN cc_start: 0.8391 (tt0) cc_final: 0.7600 (mt0) REVERT: E 247 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7284 (tm-30) REVERT: E 349 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8035 (mp) REVERT: E 403 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7371 (ttt-90) REVERT: E 485 SER cc_start: 0.7972 (t) cc_final: 0.7542 (t) REVERT: E 486 ASN cc_start: 0.8069 (t0) cc_final: 0.7845 (t0) REVERT: E 544 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7224 (tm-30) REVERT: E 694 LYS cc_start: 0.8461 (tmtt) cc_final: 0.7947 (tmtt) REVERT: F 156 ASN cc_start: 0.7481 (m110) cc_final: 0.7171 (m110) REVERT: F 196 GLU cc_start: 0.7579 (tm-30) cc_final: 0.6754 (tm-30) REVERT: F 197 GLU cc_start: 0.7285 (mp0) cc_final: 0.7027 (mp0) REVERT: F 200 GLN cc_start: 0.8476 (tt0) cc_final: 0.7973 (mt0) REVERT: F 201 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7709 (mtp85) REVERT: F 209 ASP cc_start: 0.7981 (t0) cc_final: 0.7629 (t0) REVERT: F 212 LEU cc_start: 0.8259 (mt) cc_final: 0.7892 (mp) REVERT: F 232 ASN cc_start: 0.8284 (m-40) cc_final: 0.8057 (m-40) REVERT: F 247 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7215 (tm-30) REVERT: F 249 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7910 (mmm-85) REVERT: F 352 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7781 (mm-30) REVERT: F 444 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8633 (mt) REVERT: F 454 ASP cc_start: 0.7782 (m-30) cc_final: 0.7448 (m-30) REVERT: F 484 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7244 (ttp80) REVERT: F 485 SER cc_start: 0.8130 (t) cc_final: 0.7549 (t) REVERT: F 520 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7151 (tm-30) REVERT: F 540 THR cc_start: 0.8732 (t) cc_final: 0.8466 (t) REVERT: F 544 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 587 HIS cc_start: 0.8329 (m90) cc_final: 0.8122 (m-70) REVERT: F 592 PHE cc_start: 0.7770 (t80) cc_final: 0.7527 (t80) REVERT: F 609 GLN cc_start: 0.8076 (tp40) cc_final: 0.7470 (tp40) REVERT: F 612 MET cc_start: 0.7713 (tpp) cc_final: 0.6983 (tpp) REVERT: F 638 TRP cc_start: 0.7159 (m-90) cc_final: 0.6829 (m-90) REVERT: F 694 LYS cc_start: 0.8408 (tmtt) cc_final: 0.7970 (tptp) REVERT: G 100 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: G 155 GLU cc_start: 0.7314 (mp0) cc_final: 0.7021 (mp0) REVERT: G 157 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7974 (ttm110) REVERT: G 189 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8013 (tm-30) REVERT: G 195 SER cc_start: 0.8131 (m) cc_final: 0.7740 (t) REVERT: G 196 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6737 (tm-30) REVERT: G 247 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7347 (tm-30) REVERT: G 349 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8088 (mp) REVERT: G 376 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6723 (mtt-85) REVERT: G 520 GLU cc_start: 0.7515 (tp30) cc_final: 0.7256 (tp30) REVERT: G 521 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7490 (tp-100) REVERT: G 525 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7566 (mm-30) REVERT: G 694 LYS cc_start: 0.8427 (tmtt) cc_final: 0.7895 (tmtt) REVERT: H 156 ASN cc_start: 0.7567 (m110) cc_final: 0.7252 (m110) REVERT: H 159 ARG cc_start: 0.8456 (tpt90) cc_final: 0.8017 (tpt90) REVERT: H 196 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7258 (tm-30) REVERT: H 197 GLU cc_start: 0.7414 (mp0) cc_final: 0.7087 (mp0) REVERT: H 209 ASP cc_start: 0.8066 (t0) cc_final: 0.7674 (t0) REVERT: H 247 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7286 (tm-30) REVERT: H 249 ARG cc_start: 0.8312 (tpp80) cc_final: 0.8053 (mmm-85) REVERT: H 282 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: H 303 LEU cc_start: 0.8519 (mp) cc_final: 0.8287 (mm) REVERT: H 352 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7725 (mm-30) REVERT: H 363 LYS cc_start: 0.7537 (mppt) cc_final: 0.7058 (mppt) REVERT: H 416 GLU cc_start: 0.6582 (mp0) cc_final: 0.6312 (mp0) REVERT: H 444 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8637 (mt) REVERT: H 454 ASP cc_start: 0.7821 (m-30) cc_final: 0.7471 (m-30) REVERT: H 485 SER cc_start: 0.8281 (t) cc_final: 0.7839 (t) REVERT: H 540 THR cc_start: 0.8571 (m) cc_final: 0.8134 (t) REVERT: H 544 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7395 (tm-30) REVERT: H 592 PHE cc_start: 0.7978 (t80) cc_final: 0.7664 (t80) REVERT: H 609 GLN cc_start: 0.7909 (tp40) cc_final: 0.7342 (tp40) REVERT: H 693 GLU cc_start: 0.7499 (tp30) cc_final: 0.7168 (tp30) REVERT: H 694 LYS cc_start: 0.8503 (tptt) cc_final: 0.8218 (tptt) outliers start: 147 outliers final: 107 residues processed: 1126 average time/residue: 0.2755 time to fit residues: 473.6792 Evaluate side-chains 1141 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1019 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 295 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 470 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 422 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 585 GLN D 685 HIS ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 522 GLN F 585 GLN G 422 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN H 423 GLN H 522 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127222 restraints weight = 56268.921| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.41 r_work: 0.3502 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37552 Z= 0.140 Angle : 0.648 14.103 50728 Z= 0.316 Chirality : 0.041 0.253 5848 Planarity : 0.004 0.048 6536 Dihedral : 4.344 23.061 5128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.55 % Allowed : 19.92 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 4624 helix: 0.56 (0.10), residues: 3160 sheet: -2.28 (0.39), residues: 160 loop : -1.70 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 289 TYR 0.019 0.001 TYR A 380 PHE 0.055 0.001 PHE E 96 TRP 0.010 0.001 TRP E 103 HIS 0.013 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00320 (37552) covalent geometry : angle 0.64756 (50728) hydrogen bonds : bond 0.04362 ( 1882) hydrogen bonds : angle 4.12007 ( 5574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1051 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8156 (ttm110) REVERT: A 195 SER cc_start: 0.8054 (m) cc_final: 0.7658 (t) REVERT: A 196 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6634 (tm-30) REVERT: A 197 GLU cc_start: 0.7285 (mp0) cc_final: 0.6997 (mp0) REVERT: A 200 GLN cc_start: 0.8332 (tt0) cc_final: 0.8101 (tt0) REVERT: A 376 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6835 (mtm-85) REVERT: A 413 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7938 (mmtp) REVERT: A 479 TYR cc_start: 0.8190 (m-80) cc_final: 0.7860 (m-80) REVERT: A 484 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7588 (mmm-85) REVERT: A 485 SER cc_start: 0.8153 (t) cc_final: 0.7666 (t) REVERT: A 520 GLU cc_start: 0.7561 (tp30) cc_final: 0.7122 (tp30) REVERT: A 586 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 592 PHE cc_start: 0.7614 (t80) cc_final: 0.7288 (t80) REVERT: A 609 GLN cc_start: 0.8313 (tp40) cc_final: 0.7651 (tp40) REVERT: A 682 LYS cc_start: 0.7037 (tptp) cc_final: 0.6655 (tptp) REVERT: A 694 LYS cc_start: 0.8391 (tmtt) cc_final: 0.7889 (tptp) REVERT: B 100 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: B 156 ASN cc_start: 0.7653 (m110) cc_final: 0.7329 (m110) REVERT: B 189 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 196 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6330 (tm-30) REVERT: B 197 GLU cc_start: 0.7349 (mp0) cc_final: 0.7076 (mp0) REVERT: B 200 GLN cc_start: 0.8467 (tt0) cc_final: 0.7584 (mt0) REVERT: B 282 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 286 GLU cc_start: 0.7062 (tp30) cc_final: 0.6806 (tp30) REVERT: B 326 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 352 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 363 LYS cc_start: 0.7557 (mppt) cc_final: 0.7034 (mppt) REVERT: B 383 ASN cc_start: 0.8399 (t0) cc_final: 0.8036 (t0) REVERT: B 392 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8253 (ttp-170) REVERT: B 416 GLU cc_start: 0.6825 (mp0) cc_final: 0.6559 (mp0) REVERT: B 444 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 451 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 454 ASP cc_start: 0.7713 (m-30) cc_final: 0.7361 (m-30) REVERT: B 459 SER cc_start: 0.8508 (t) cc_final: 0.8222 (p) REVERT: B 484 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7330 (ttp80) REVERT: B 485 SER cc_start: 0.8281 (t) cc_final: 0.7707 (t) REVERT: B 520 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7196 (tp30) REVERT: B 540 THR cc_start: 0.8643 (t) cc_final: 0.8374 (t) REVERT: B 592 PHE cc_start: 0.7645 (t80) cc_final: 0.7393 (t80) REVERT: B 694 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8129 (tptp) REVERT: C 100 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: C 149 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 173 LYS cc_start: 0.8513 (mtmm) cc_final: 0.7723 (mtmm) REVERT: C 195 SER cc_start: 0.7989 (m) cc_final: 0.7550 (t) REVERT: C 196 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6573 (tm-30) REVERT: C 197 GLU cc_start: 0.7238 (mp0) cc_final: 0.6930 (mp0) REVERT: C 200 GLN cc_start: 0.8266 (tt0) cc_final: 0.7969 (tt0) REVERT: C 248 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8313 (mttp) REVERT: C 376 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: C 392 ARG cc_start: 0.8441 (ttm170) cc_final: 0.7960 (ttp-110) REVERT: C 413 LYS cc_start: 0.8323 (mmmm) cc_final: 0.7915 (mmtm) REVERT: C 483 ASP cc_start: 0.8125 (t0) cc_final: 0.7563 (t70) REVERT: C 520 GLU cc_start: 0.7643 (tp30) cc_final: 0.7227 (tp30) REVERT: C 694 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7724 (tmtt) REVERT: D 156 ASN cc_start: 0.7717 (m110) cc_final: 0.7335 (m110) REVERT: D 157 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7869 (mtm-85) REVERT: D 195 SER cc_start: 0.8096 (m) cc_final: 0.7682 (t) REVERT: D 196 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 197 GLU cc_start: 0.7331 (mp0) cc_final: 0.6962 (mp0) REVERT: D 209 ASP cc_start: 0.8081 (t0) cc_final: 0.7776 (t0) REVERT: D 248 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8171 (mttp) REVERT: D 282 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: D 352 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 383 ASN cc_start: 0.8270 (t0) cc_final: 0.7998 (t0) REVERT: D 395 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7591 (ttp-110) REVERT: D 416 GLU cc_start: 0.6578 (mp0) cc_final: 0.6342 (mp0) REVERT: D 444 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8602 (mt) REVERT: D 454 ASP cc_start: 0.7767 (m-30) cc_final: 0.7428 (m-30) REVERT: D 485 SER cc_start: 0.8167 (t) cc_final: 0.7664 (t) REVERT: D 540 THR cc_start: 0.8699 (t) cc_final: 0.8460 (t) REVERT: D 592 PHE cc_start: 0.7688 (t80) cc_final: 0.7472 (t80) REVERT: D 609 GLN cc_start: 0.8265 (tp40) cc_final: 0.7847 (tp40) REVERT: D 694 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7689 (tptt) REVERT: D 695 ILE cc_start: 0.8481 (pt) cc_final: 0.8181 (pt) REVERT: E 157 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.8095 (ttm110) REVERT: E 196 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6788 (tm-30) REVERT: E 197 GLU cc_start: 0.7230 (mp0) cc_final: 0.7021 (mp0) REVERT: E 247 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7261 (tm-30) REVERT: E 376 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.7129 (mtt-85) REVERT: E 403 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7312 (ttt-90) REVERT: E 485 SER cc_start: 0.8074 (t) cc_final: 0.7628 (t) REVERT: E 544 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7234 (tm-30) REVERT: E 694 LYS cc_start: 0.8433 (tmtt) cc_final: 0.7781 (tmtt) REVERT: F 156 ASN cc_start: 0.7481 (m110) cc_final: 0.7159 (m110) REVERT: F 196 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6756 (tm-30) REVERT: F 197 GLU cc_start: 0.7305 (mp0) cc_final: 0.7027 (mp0) REVERT: F 200 GLN cc_start: 0.8497 (tt0) cc_final: 0.7921 (mt0) REVERT: F 201 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7725 (mtp85) REVERT: F 209 ASP cc_start: 0.7990 (t0) cc_final: 0.7621 (t0) REVERT: F 212 LEU cc_start: 0.8182 (mt) cc_final: 0.7958 (mp) REVERT: F 232 ASN cc_start: 0.8264 (m-40) cc_final: 0.8043 (m-40) REVERT: F 247 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7276 (tm-30) REVERT: F 249 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7837 (mmm-85) REVERT: F 352 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7784 (mm-30) REVERT: F 444 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8650 (mt) REVERT: F 454 ASP cc_start: 0.7774 (m-30) cc_final: 0.7461 (m-30) REVERT: F 484 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7227 (ttp80) REVERT: F 485 SER cc_start: 0.8163 (t) cc_final: 0.7591 (t) REVERT: F 520 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7161 (tm-30) REVERT: F 540 THR cc_start: 0.8734 (t) cc_final: 0.8459 (t) REVERT: F 544 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7461 (tm-30) REVERT: F 592 PHE cc_start: 0.7808 (t80) cc_final: 0.7552 (t80) REVERT: F 609 GLN cc_start: 0.8150 (tp40) cc_final: 0.7534 (tp40) REVERT: F 612 MET cc_start: 0.7776 (tpp) cc_final: 0.7039 (tpp) REVERT: F 638 TRP cc_start: 0.7224 (m-90) cc_final: 0.6919 (m-90) REVERT: F 694 LYS cc_start: 0.8394 (tmtt) cc_final: 0.7967 (tptp) REVERT: G 100 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: G 155 GLU cc_start: 0.7235 (mp0) cc_final: 0.6933 (mp0) REVERT: G 157 ARG cc_start: 0.8232 (mtp180) cc_final: 0.8013 (ttm110) REVERT: G 189 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8012 (tm-30) REVERT: G 196 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6909 (tm-30) REVERT: G 247 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7352 (tm-30) REVERT: G 376 ARG cc_start: 0.7041 (mtt-85) cc_final: 0.6705 (mtt-85) REVERT: G 392 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8121 (ttp-110) REVERT: G 520 GLU cc_start: 0.7530 (tp30) cc_final: 0.7141 (tp30) REVERT: G 525 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7606 (mm-30) REVERT: G 694 LYS cc_start: 0.8414 (tmtt) cc_final: 0.7866 (tmtt) REVERT: H 156 ASN cc_start: 0.7565 (m110) cc_final: 0.7241 (m110) REVERT: H 159 ARG cc_start: 0.8490 (tpt90) cc_final: 0.8050 (tpt90) REVERT: H 196 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7262 (tm-30) REVERT: H 197 GLU cc_start: 0.7452 (mp0) cc_final: 0.7105 (mp0) REVERT: H 209 ASP cc_start: 0.8055 (t0) cc_final: 0.7654 (t0) REVERT: H 247 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7297 (tm-30) REVERT: H 249 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8024 (mmm-85) REVERT: H 282 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: H 286 GLU cc_start: 0.7287 (tp30) cc_final: 0.7023 (tp30) REVERT: H 303 LEU cc_start: 0.8503 (mp) cc_final: 0.8278 (mm) REVERT: H 352 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7720 (mm-30) REVERT: H 363 LYS cc_start: 0.7533 (mppt) cc_final: 0.7070 (mppt) REVERT: H 416 GLU cc_start: 0.6641 (mp0) cc_final: 0.6341 (mp0) REVERT: H 444 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8625 (mt) REVERT: H 454 ASP cc_start: 0.7778 (m-30) cc_final: 0.7443 (m-30) REVERT: H 540 THR cc_start: 0.8562 (m) cc_final: 0.8071 (t) REVERT: H 544 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7391 (tm-30) REVERT: H 609 GLN cc_start: 0.7967 (tp40) cc_final: 0.7444 (tp40) REVERT: H 693 GLU cc_start: 0.7554 (tp30) cc_final: 0.7209 (tp30) REVERT: H 694 LYS cc_start: 0.8520 (tptt) cc_final: 0.8232 (tptt) outliers start: 139 outliers final: 96 residues processed: 1119 average time/residue: 0.2784 time to fit residues: 474.6813 Evaluate side-chains 1107 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 998 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 110 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 69 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 144 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 422 GLN A 522 GLN A 585 GLN A 587 HIS B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 585 GLN D 685 HIS ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 522 GLN F 585 GLN G 422 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN H 423 GLN H 522 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.153802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127324 restraints weight = 56531.157| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.42 r_work: 0.3506 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37552 Z= 0.136 Angle : 0.658 12.677 50728 Z= 0.319 Chirality : 0.041 0.158 5848 Planarity : 0.004 0.048 6536 Dihedral : 4.306 22.983 5128 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.32 % Allowed : 20.69 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.13), residues: 4624 helix: 0.61 (0.10), residues: 3160 sheet: -2.19 (0.40), residues: 160 loop : -1.66 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 289 TYR 0.019 0.001 TYR A 380 PHE 0.042 0.001 PHE E 96 TRP 0.010 0.001 TRP E 103 HIS 0.015 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00313 (37552) covalent geometry : angle 0.65836 (50728) hydrogen bonds : bond 0.04221 ( 1882) hydrogen bonds : angle 4.06942 ( 5574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1051 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8133 (ttm110) REVERT: A 195 SER cc_start: 0.8064 (m) cc_final: 0.7663 (t) REVERT: A 196 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 197 GLU cc_start: 0.7295 (mp0) cc_final: 0.6998 (mp0) REVERT: A 200 GLN cc_start: 0.8328 (tt0) cc_final: 0.8077 (tt0) REVERT: A 209 ASP cc_start: 0.8022 (t0) cc_final: 0.7579 (t0) REVERT: A 376 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6784 (mtm-85) REVERT: A 392 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8070 (ttp-110) REVERT: A 413 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7882 (mmtm) REVERT: A 479 TYR cc_start: 0.8183 (m-80) cc_final: 0.7852 (m-80) REVERT: A 484 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7625 (mmm-85) REVERT: A 520 GLU cc_start: 0.7573 (tp30) cc_final: 0.7133 (tp30) REVERT: A 586 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 592 PHE cc_start: 0.7592 (t80) cc_final: 0.7272 (t80) REVERT: A 609 GLN cc_start: 0.8292 (tp40) cc_final: 0.7625 (tp40) REVERT: A 682 LYS cc_start: 0.7098 (tptp) cc_final: 0.6709 (tptp) REVERT: A 694 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8045 (tptp) REVERT: B 100 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: B 156 ASN cc_start: 0.7663 (m110) cc_final: 0.7328 (m110) REVERT: B 189 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 196 GLU cc_start: 0.7557 (tm-30) cc_final: 0.6336 (tm-30) REVERT: B 197 GLU cc_start: 0.7351 (mp0) cc_final: 0.7065 (mp0) REVERT: B 200 GLN cc_start: 0.8451 (tt0) cc_final: 0.7562 (mt0) REVERT: B 282 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: B 286 GLU cc_start: 0.7096 (tp30) cc_final: 0.6844 (tp30) REVERT: B 326 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7276 (t0) REVERT: B 352 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 363 LYS cc_start: 0.7500 (mppt) cc_final: 0.6987 (mppt) REVERT: B 383 ASN cc_start: 0.8385 (t0) cc_final: 0.7999 (t0) REVERT: B 392 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.8230 (ttp-170) REVERT: B 416 GLU cc_start: 0.6860 (mp0) cc_final: 0.6571 (mp0) REVERT: B 444 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 451 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7802 (mt) REVERT: B 454 ASP cc_start: 0.7711 (m-30) cc_final: 0.7349 (m-30) REVERT: B 459 SER cc_start: 0.8490 (t) cc_final: 0.8196 (p) REVERT: B 484 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7335 (ttp80) REVERT: B 485 SER cc_start: 0.8303 (t) cc_final: 0.7731 (t) REVERT: B 520 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 540 THR cc_start: 0.8626 (t) cc_final: 0.8351 (t) REVERT: B 592 PHE cc_start: 0.7641 (t80) cc_final: 0.7385 (t80) REVERT: B 694 LYS cc_start: 0.8474 (tmtt) cc_final: 0.8135 (tptp) REVERT: C 100 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: C 149 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7112 (tp30) REVERT: C 173 LYS cc_start: 0.8524 (mtmm) cc_final: 0.7714 (mtmm) REVERT: C 195 SER cc_start: 0.7963 (m) cc_final: 0.7630 (t) REVERT: C 196 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6500 (tm-30) REVERT: C 197 GLU cc_start: 0.7232 (mp0) cc_final: 0.6968 (mp0) REVERT: C 200 GLN cc_start: 0.8261 (tt0) cc_final: 0.8010 (tt0) REVERT: C 248 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8304 (mttp) REVERT: C 376 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6855 (mtm-85) REVERT: C 392 ARG cc_start: 0.8430 (ttm170) cc_final: 0.7932 (ttp-110) REVERT: C 483 ASP cc_start: 0.8121 (t0) cc_final: 0.7475 (t0) REVERT: C 520 GLU cc_start: 0.7648 (tp30) cc_final: 0.7225 (tp30) REVERT: C 694 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7721 (tmtt) REVERT: D 156 ASN cc_start: 0.7715 (m110) cc_final: 0.7326 (m110) REVERT: D 157 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7835 (mtm-85) REVERT: D 189 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 195 SER cc_start: 0.8083 (m) cc_final: 0.7665 (t) REVERT: D 196 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 197 GLU cc_start: 0.7341 (mp0) cc_final: 0.6957 (mp0) REVERT: D 209 ASP cc_start: 0.8061 (t0) cc_final: 0.7786 (t0) REVERT: D 248 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8135 (mttp) REVERT: D 282 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: D 352 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7788 (mm-30) REVERT: D 392 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8100 (ttp-110) REVERT: D 395 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7595 (ttp-110) REVERT: D 416 GLU cc_start: 0.6641 (mp0) cc_final: 0.6390 (mp0) REVERT: D 418 GLN cc_start: 0.8444 (mm110) cc_final: 0.7907 (mm110) REVERT: D 444 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8618 (mt) REVERT: D 485 SER cc_start: 0.8182 (t) cc_final: 0.7687 (t) REVERT: D 495 ASP cc_start: 0.7880 (t0) cc_final: 0.7640 (t0) REVERT: D 540 THR cc_start: 0.8663 (t) cc_final: 0.8417 (t) REVERT: D 592 PHE cc_start: 0.7677 (t80) cc_final: 0.7466 (t80) REVERT: D 609 GLN cc_start: 0.8254 (tp40) cc_final: 0.7840 (tp40) REVERT: D 694 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7721 (tptt) REVERT: D 695 ILE cc_start: 0.8496 (pt) cc_final: 0.8196 (pt) REVERT: E 157 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.8089 (ttm110) REVERT: E 196 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6786 (tm-30) REVERT: E 247 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 423 GLN cc_start: 0.8408 (mt0) cc_final: 0.7887 (tt0) REVERT: E 485 SER cc_start: 0.8113 (t) cc_final: 0.7651 (t) REVERT: E 519 SER cc_start: 0.8614 (t) cc_final: 0.8099 (p) REVERT: E 544 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 694 LYS cc_start: 0.8432 (tmtt) cc_final: 0.7782 (tmtt) REVERT: F 156 ASN cc_start: 0.7491 (m110) cc_final: 0.7157 (m110) REVERT: F 196 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6712 (tm-30) REVERT: F 197 GLU cc_start: 0.7299 (mp0) cc_final: 0.7033 (mp0) REVERT: F 200 GLN cc_start: 0.8509 (tt0) cc_final: 0.7913 (mt0) REVERT: F 201 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7733 (mtp85) REVERT: F 209 ASP cc_start: 0.8019 (t0) cc_final: 0.7648 (t0) REVERT: F 212 LEU cc_start: 0.8147 (mt) cc_final: 0.7917 (mp) REVERT: F 247 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7253 (tm-30) REVERT: F 249 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7831 (mmm-85) REVERT: F 352 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7794 (mm-30) REVERT: F 444 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8651 (mt) REVERT: F 448 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7142 (mm-30) REVERT: F 454 ASP cc_start: 0.7649 (m-30) cc_final: 0.7422 (m-30) REVERT: F 484 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7234 (ttp80) REVERT: F 520 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7172 (tm-30) REVERT: F 540 THR cc_start: 0.8795 (t) cc_final: 0.8517 (t) REVERT: F 544 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7460 (tm-30) REVERT: F 592 PHE cc_start: 0.7819 (t80) cc_final: 0.7560 (t80) REVERT: F 609 GLN cc_start: 0.8110 (tp40) cc_final: 0.7482 (tp40) REVERT: F 612 MET cc_start: 0.7731 (tpp) cc_final: 0.6992 (tpp) REVERT: F 638 TRP cc_start: 0.7251 (m-90) cc_final: 0.6939 (m-90) REVERT: F 694 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7985 (tptp) REVERT: G 100 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: G 157 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7991 (ttm110) REVERT: G 189 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8008 (tm-30) REVERT: G 196 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6914 (tm-30) REVERT: G 247 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7331 (tm-30) REVERT: G 349 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8064 (mp) REVERT: G 376 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6715 (mtt-85) REVERT: G 392 ARG cc_start: 0.8559 (ttm170) cc_final: 0.8138 (ttp-110) REVERT: G 694 LYS cc_start: 0.8498 (tmtt) cc_final: 0.7949 (tmtt) REVERT: H 156 ASN cc_start: 0.7576 (m110) cc_final: 0.7241 (m110) REVERT: H 159 ARG cc_start: 0.8484 (tpt90) cc_final: 0.8126 (tpt90) REVERT: H 196 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7263 (tm-30) REVERT: H 197 GLU cc_start: 0.7364 (mp0) cc_final: 0.7027 (mp0) REVERT: H 209 ASP cc_start: 0.8057 (t0) cc_final: 0.7662 (t0) REVERT: H 247 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7303 (tm-30) REVERT: H 249 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8022 (mmm-85) REVERT: H 282 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: H 352 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7556 (mm-30) REVERT: H 363 LYS cc_start: 0.7518 (mppt) cc_final: 0.7073 (mppt) REVERT: H 416 GLU cc_start: 0.6670 (mp0) cc_final: 0.6376 (mp0) REVERT: H 444 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8633 (mt) REVERT: H 454 ASP cc_start: 0.7750 (m-30) cc_final: 0.7390 (m-30) REVERT: H 540 THR cc_start: 0.8552 (m) cc_final: 0.8070 (t) REVERT: H 544 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7399 (tm-30) REVERT: H 609 GLN cc_start: 0.7932 (tp40) cc_final: 0.7415 (tp40) REVERT: H 693 GLU cc_start: 0.7543 (tp30) cc_final: 0.7322 (tp30) REVERT: H 694 LYS cc_start: 0.8536 (tptt) cc_final: 0.8239 (tptt) outliers start: 130 outliers final: 98 residues processed: 1110 average time/residue: 0.2761 time to fit residues: 466.6842 Evaluate side-chains 1128 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1016 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 18 optimal weight: 2.9990 chunk 461 optimal weight: 3.9990 chunk 366 optimal weight: 0.9980 chunk 238 optimal weight: 0.0060 chunk 455 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 378 optimal weight: 0.0770 chunk 331 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 422 GLN A 585 GLN A 587 HIS B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS C 418 GLN C 422 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN D 232 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 585 GLN D 685 HIS ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 383 ASN F 522 GLN G 522 GLN G 585 GLN H 422 GLN H 423 GLN H 522 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127588 restraints weight = 56313.822| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.42 r_work: 0.3509 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37552 Z= 0.132 Angle : 0.674 17.424 50728 Z= 0.325 Chirality : 0.041 0.155 5848 Planarity : 0.004 0.048 6536 Dihedral : 4.286 22.706 5128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.06 % Allowed : 21.58 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.13), residues: 4624 helix: 0.63 (0.10), residues: 3184 sheet: -2.14 (0.40), residues: 160 loop : -1.59 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 289 TYR 0.021 0.001 TYR A 380 PHE 0.038 0.001 PHE E 96 TRP 0.009 0.001 TRP A 638 HIS 0.020 0.001 HIS B 685 Details of bonding type rmsd covalent geometry : bond 0.00304 (37552) covalent geometry : angle 0.67367 (50728) hydrogen bonds : bond 0.04141 ( 1882) hydrogen bonds : angle 4.03182 ( 5574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1055 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 111 GLU cc_start: 0.8009 (tp30) cc_final: 0.7770 (mm-30) REVERT: A 157 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8126 (ttm110) REVERT: A 195 SER cc_start: 0.8073 (m) cc_final: 0.7681 (t) REVERT: A 196 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 197 GLU cc_start: 0.7296 (mp0) cc_final: 0.6998 (mp0) REVERT: A 200 GLN cc_start: 0.8345 (tt0) cc_final: 0.8082 (tt0) REVERT: A 209 ASP cc_start: 0.8033 (t0) cc_final: 0.7606 (t0) REVERT: A 376 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6827 (mtm-85) REVERT: A 392 ARG cc_start: 0.8468 (ttm170) cc_final: 0.8064 (ttp-110) REVERT: A 413 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7887 (mmtm) REVERT: A 423 GLN cc_start: 0.8379 (mt0) cc_final: 0.8112 (tt0) REVERT: A 484 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7595 (mmm-85) REVERT: A 511 ASP cc_start: 0.7900 (p0) cc_final: 0.7670 (p0) REVERT: A 520 GLU cc_start: 0.7579 (tp30) cc_final: 0.7121 (tp30) REVERT: A 586 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8464 (mm) REVERT: A 592 PHE cc_start: 0.7590 (t80) cc_final: 0.7263 (t80) REVERT: A 609 GLN cc_start: 0.8296 (tp40) cc_final: 0.7597 (tp40) REVERT: A 682 LYS cc_start: 0.7098 (tptp) cc_final: 0.6703 (tptp) REVERT: A 694 LYS cc_start: 0.8415 (tmtt) cc_final: 0.8044 (tptp) REVERT: B 100 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 149 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 156 ASN cc_start: 0.7660 (m110) cc_final: 0.7330 (m110) REVERT: B 189 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 196 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6321 (tm-30) REVERT: B 197 GLU cc_start: 0.7361 (mp0) cc_final: 0.7067 (mp0) REVERT: B 200 GLN cc_start: 0.8465 (tt0) cc_final: 0.7569 (mt0) REVERT: B 282 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: B 286 GLU cc_start: 0.7166 (tp30) cc_final: 0.6938 (tp30) REVERT: B 326 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 352 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 363 LYS cc_start: 0.7471 (mppt) cc_final: 0.6941 (mppt) REVERT: B 383 ASN cc_start: 0.8359 (t0) cc_final: 0.7983 (t0) REVERT: B 392 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.8280 (ttp-170) REVERT: B 416 GLU cc_start: 0.6867 (mp0) cc_final: 0.6581 (mp0) REVERT: B 422 GLN cc_start: 0.8403 (mt0) cc_final: 0.8065 (tt0) REVERT: B 444 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 451 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7817 (mt) REVERT: B 454 ASP cc_start: 0.7691 (m-30) cc_final: 0.7324 (m-30) REVERT: B 485 SER cc_start: 0.8302 (t) cc_final: 0.7826 (t) REVERT: B 540 THR cc_start: 0.8624 (t) cc_final: 0.8344 (t) REVERT: B 592 PHE cc_start: 0.7665 (t80) cc_final: 0.7397 (t80) REVERT: B 694 LYS cc_start: 0.8494 (tmtt) cc_final: 0.8148 (tptp) REVERT: C 100 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: C 149 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7128 (tp30) REVERT: C 173 LYS cc_start: 0.8530 (mtmm) cc_final: 0.7687 (mtmm) REVERT: C 195 SER cc_start: 0.7958 (m) cc_final: 0.7626 (t) REVERT: C 196 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6573 (tm-30) REVERT: C 197 GLU cc_start: 0.7231 (mp0) cc_final: 0.6989 (mp0) REVERT: C 200 GLN cc_start: 0.8282 (tt0) cc_final: 0.8023 (tt0) REVERT: C 248 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8305 (mttp) REVERT: C 376 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6837 (mtm-85) REVERT: C 392 ARG cc_start: 0.8443 (ttm170) cc_final: 0.7949 (ttp-110) REVERT: C 413 LYS cc_start: 0.8310 (mmmm) cc_final: 0.7897 (mmtm) REVERT: C 423 GLN cc_start: 0.8402 (mt0) cc_final: 0.7955 (tt0) REVERT: C 483 ASP cc_start: 0.8114 (t0) cc_final: 0.7460 (t0) REVERT: C 520 GLU cc_start: 0.7626 (tp30) cc_final: 0.7197 (tp30) REVERT: C 693 GLU cc_start: 0.7491 (tp30) cc_final: 0.7151 (tp30) REVERT: C 694 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7713 (tmtt) REVERT: D 156 ASN cc_start: 0.7710 (m110) cc_final: 0.7397 (m110) REVERT: D 157 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7843 (mtm-85) REVERT: D 189 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8016 (tm-30) REVERT: D 195 SER cc_start: 0.8077 (m) cc_final: 0.7641 (t) REVERT: D 196 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6989 (tm-30) REVERT: D 197 GLU cc_start: 0.7351 (mp0) cc_final: 0.6965 (mp0) REVERT: D 209 ASP cc_start: 0.8109 (t0) cc_final: 0.7826 (t0) REVERT: D 247 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7342 (tm-30) REVERT: D 248 LYS cc_start: 0.8455 (mmtp) cc_final: 0.8069 (mttp) REVERT: D 282 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: D 352 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7762 (mm-30) REVERT: D 363 LYS cc_start: 0.7526 (mppt) cc_final: 0.7148 (mppt) REVERT: D 392 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.8133 (ttp-110) REVERT: D 395 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7605 (ttp-110) REVERT: D 416 GLU cc_start: 0.6654 (mp0) cc_final: 0.6399 (mp0) REVERT: D 444 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8619 (mt) REVERT: D 449 GLU cc_start: 0.7473 (pm20) cc_final: 0.7246 (pm20) REVERT: D 485 SER cc_start: 0.8179 (t) cc_final: 0.7682 (t) REVERT: D 495 ASP cc_start: 0.7882 (t0) cc_final: 0.7648 (t0) REVERT: D 540 THR cc_start: 0.8668 (t) cc_final: 0.8421 (t) REVERT: D 592 PHE cc_start: 0.7676 (t80) cc_final: 0.7457 (t80) REVERT: D 609 GLN cc_start: 0.8262 (tp40) cc_final: 0.7837 (tp40) REVERT: D 694 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7697 (tptt) REVERT: D 695 ILE cc_start: 0.8476 (pt) cc_final: 0.8172 (pt) REVERT: E 157 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8072 (ttm110) REVERT: E 196 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6804 (tm-30) REVERT: E 247 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 423 GLN cc_start: 0.8387 (mt0) cc_final: 0.7879 (tt0) REVERT: E 485 SER cc_start: 0.8127 (t) cc_final: 0.7669 (t) REVERT: E 519 SER cc_start: 0.8596 (t) cc_final: 0.8096 (p) REVERT: E 520 GLU cc_start: 0.7713 (tp30) cc_final: 0.7469 (tp30) REVERT: E 544 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7250 (tm-30) REVERT: E 694 LYS cc_start: 0.8435 (tmtt) cc_final: 0.7770 (tmtt) REVERT: F 156 ASN cc_start: 0.7512 (m110) cc_final: 0.7177 (m110) REVERT: F 165 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (tp) REVERT: F 196 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6802 (tm-30) REVERT: F 197 GLU cc_start: 0.7325 (mp0) cc_final: 0.7070 (mp0) REVERT: F 200 GLN cc_start: 0.8505 (tt0) cc_final: 0.7918 (mt0) REVERT: F 201 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7725 (mtp85) REVERT: F 209 ASP cc_start: 0.7996 (t0) cc_final: 0.7627 (t0) REVERT: F 212 LEU cc_start: 0.8146 (mt) cc_final: 0.7931 (mp) REVERT: F 247 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7265 (tm-30) REVERT: F 249 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7820 (mmm-85) REVERT: F 352 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 383 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8156 (t0) REVERT: F 444 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8653 (mt) REVERT: F 448 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6903 (tp30) REVERT: F 484 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7260 (ttp80) REVERT: F 520 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7169 (tm-30) REVERT: F 540 THR cc_start: 0.8756 (t) cc_final: 0.8491 (t) REVERT: F 544 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7468 (tm-30) REVERT: F 592 PHE cc_start: 0.7821 (t80) cc_final: 0.7569 (t80) REVERT: F 609 GLN cc_start: 0.8142 (tp40) cc_final: 0.7525 (tp40) REVERT: F 612 MET cc_start: 0.7702 (tpp) cc_final: 0.6989 (tpp) REVERT: F 638 TRP cc_start: 0.7251 (m-90) cc_final: 0.6852 (m-90) REVERT: F 694 LYS cc_start: 0.8390 (tmtt) cc_final: 0.7992 (tptp) REVERT: G 100 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: G 155 GLU cc_start: 0.7353 (mp0) cc_final: 0.7069 (mp0) REVERT: G 157 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7981 (ttm110) REVERT: G 189 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8000 (tm-30) REVERT: G 196 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6929 (tm-30) REVERT: G 247 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7341 (tm-30) REVERT: G 376 ARG cc_start: 0.7106 (mtt-85) cc_final: 0.6826 (mtt-85) REVERT: G 392 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8181 (ttp-110) REVERT: G 448 GLU cc_start: 0.7600 (tt0) cc_final: 0.7396 (tt0) REVERT: G 454 ASP cc_start: 0.7664 (m-30) cc_final: 0.7411 (m-30) REVERT: G 520 GLU cc_start: 0.7528 (tp30) cc_final: 0.7126 (tp30) REVERT: G 693 GLU cc_start: 0.7640 (tp30) cc_final: 0.7229 (tp30) REVERT: G 694 LYS cc_start: 0.8494 (tmtt) cc_final: 0.7919 (tmtt) REVERT: H 156 ASN cc_start: 0.7568 (m110) cc_final: 0.7239 (m110) REVERT: H 159 ARG cc_start: 0.8501 (tpt90) cc_final: 0.8152 (tpt90) REVERT: H 196 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 197 GLU cc_start: 0.7365 (mp0) cc_final: 0.7032 (mp0) REVERT: H 209 ASP cc_start: 0.8043 (t0) cc_final: 0.7642 (t0) REVERT: H 247 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7284 (tm-30) REVERT: H 249 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8029 (mmm-85) REVERT: H 282 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: H 352 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7572 (mm-30) REVERT: H 363 LYS cc_start: 0.7525 (mppt) cc_final: 0.7256 (tppt) REVERT: H 416 GLU cc_start: 0.6669 (mp0) cc_final: 0.6387 (mp0) REVERT: H 444 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8623 (mt) REVERT: H 454 ASP cc_start: 0.7726 (m-30) cc_final: 0.7519 (m-30) REVERT: H 540 THR cc_start: 0.8548 (m) cc_final: 0.8064 (t) REVERT: H 544 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7411 (tm-30) REVERT: H 609 GLN cc_start: 0.7915 (tp40) cc_final: 0.7402 (tp40) REVERT: H 693 GLU cc_start: 0.7566 (tp30) cc_final: 0.7164 (tp30) REVERT: H 694 LYS cc_start: 0.8541 (tptt) cc_final: 0.8216 (tptt) outliers start: 120 outliers final: 98 residues processed: 1110 average time/residue: 0.2472 time to fit residues: 420.1399 Evaluate side-chains 1132 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1018 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 ASN Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 531 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 124 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 203 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 chunk 450 optimal weight: 1.9990 chunk 455 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 411 optimal weight: 0.9980 chunk 437 optimal weight: 1.9990 chunk 387 optimal weight: 0.0040 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 422 GLN A 585 GLN A 587 HIS B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 422 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN D 232 ASN D 383 ASN D 422 GLN D 585 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 383 ASN F 522 GLN G 418 GLN G 522 GLN G 585 GLN H 422 GLN H 423 GLN H 522 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127407 restraints weight = 56245.893| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.41 r_work: 0.3511 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 37552 Z= 0.167 Angle : 0.757 59.182 50728 Z= 0.391 Chirality : 0.045 1.422 5848 Planarity : 0.005 0.123 6536 Dihedral : 4.294 22.703 5128 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.98 % Allowed : 21.99 % Favored : 75.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.13), residues: 4624 helix: 0.63 (0.10), residues: 3184 sheet: -2.14 (0.40), residues: 160 loop : -1.58 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 289 TYR 0.019 0.001 TYR A 380 PHE 0.032 0.001 PHE E 96 TRP 0.014 0.001 TRP E 638 HIS 0.129 0.002 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00377 (37552) covalent geometry : angle 0.75684 (50728) hydrogen bonds : bond 0.04141 ( 1882) hydrogen bonds : angle 4.03505 ( 5574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10673.23 seconds wall clock time: 182 minutes 56.35 seconds (10976.35 seconds total)