Starting phenix.real_space_refine on Thu Mar 5 06:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4e_22666/03_2026/7k4e_22666.map" } resolution = 4.34 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= 0.019 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 164 5.16 5 C 13027 2.51 5 N 3415 2.21 5 O 3513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20119 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "C" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "D" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'VUJ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.24 Number of scatterers: 20119 At special positions: 0 Unit cell: (145.35, 145.35, 127.3, 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 164 16.00 O 3513 8.00 N 3415 7.00 C 13027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 982.5 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 61.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 removed outlier: 4.175A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.898A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.970A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.928A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.795A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.519A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.825A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.939A pdb=" N ARG A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.671A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.649A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.675A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.961A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 4.162A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.615A pdb=" N PHE A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.865A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.604A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 4.028A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.578A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.805A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.813A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 446 removed outlier: 4.124A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.586A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.956A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 510 removed outlier: 4.045A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 4.058A pdb=" N THR A 514 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 515 " --> pdb=" O PHE A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.549A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.932A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.773A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.552A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 47 removed outlier: 4.174A pdb=" N GLN B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.898A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.970A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.928A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.796A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.519A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.825A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.938A pdb=" N ARG B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 removed outlier: 3.671A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.650A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.676A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.961A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 4.162A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.615A pdb=" N PHE B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.866A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.604A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 removed outlier: 4.028A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.577A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 removed outlier: 3.805A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 removed outlier: 3.813A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 446 removed outlier: 4.125A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.585A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.957A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 510 removed outlier: 4.044A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 4.059A pdb=" N THR B 514 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 515 " --> pdb=" O PHE B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.548A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 3.931A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 3.772A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.552A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 4.174A pdb=" N GLN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.898A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.970A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.928A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.794A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.519A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.825A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.938A pdb=" N ARG C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.671A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.650A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.675A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.961A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 4.162A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.614A pdb=" N PHE C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.866A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.603A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 4.028A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 3.578A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 343 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.805A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 423 removed outlier: 3.813A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 446 removed outlier: 4.124A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 438 " --> pdb=" O PHE C 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.585A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.956A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 510 removed outlier: 4.045A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 4.059A pdb=" N THR C 514 " --> pdb=" O ILE C 511 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 515 " --> pdb=" O PHE C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.549A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.932A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 583 removed outlier: 3.772A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 579 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.552A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 47 removed outlier: 4.175A pdb=" N GLN D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.899A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.971A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.927A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.795A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.520A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.825A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.938A pdb=" N ARG D 153 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.671A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.650A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.676A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.960A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 4.162A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.615A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.866A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.604A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 4.028A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 348 removed outlier: 3.577A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 400 removed outlier: 3.804A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 3.814A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 446 removed outlier: 4.125A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 438 " --> pdb=" O PHE D 434 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.585A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 477 through 487 removed outlier: 3.956A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 510 removed outlier: 4.045A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 4.060A pdb=" N THR D 514 " --> pdb=" O ILE D 511 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 515 " --> pdb=" O PHE D 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 515' Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.549A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 567 removed outlier: 3.932A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 584 removed outlier: 3.773A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 579 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.553A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.995A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 633 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 270 removed outlier: 4.994A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 633 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 270 removed outlier: 4.994A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 633 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 270 removed outlier: 4.994A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL D 633 " --> pdb=" O THR D 276 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.11 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: 6330 1.34 - 1.46: 4040 1.46 - 1.58: 9953 1.58 - 1.69: 3 1.69 - 1.81: 276 Bond restraints: 20602 Sorted by residual: bond pdb=" C22 VUJ B 701 " pdb=" C23 VUJ B 701 " ideal model delta sigma weight residual 1.330 1.539 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C22 VUJ D 701 " pdb=" C23 VUJ D 701 " ideal model delta sigma weight residual 1.330 1.538 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C22 VUJ A 701 " pdb=" C23 VUJ A 701 " ideal model delta sigma weight residual 1.330 1.538 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C22 VUJ C 701 " pdb=" C23 VUJ C 701 " ideal model delta sigma weight residual 1.330 1.537 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C22 VUJ B 702 " pdb=" C23 VUJ B 702 " ideal model delta sigma weight residual 1.330 1.535 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 20597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 27168 2.76 - 5.52: 632 5.52 - 8.27: 93 8.27 - 11.03: 44 11.03 - 13.79: 8 Bond angle restraints: 27945 Sorted by residual: angle pdb=" C TYR D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C TYR A 89 " pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C TYR C 89 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " pdb=" CG ARG C 140 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 27940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 11956 22.52 - 45.03: 431 45.03 - 67.55: 24 67.55 - 90.07: 15 90.07 - 112.58: 2 Dihedral angle restraints: 12428 sinusoidal: 5172 harmonic: 7256 Sorted by residual: dihedral pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta harmonic sigma weight residual -180.00 -135.31 -44.69 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA GLN D 230 " pdb=" C GLN D 230 " pdb=" N PRO D 231 " pdb=" CA PRO D 231 " ideal model delta harmonic sigma weight residual -180.00 -135.32 -44.68 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA GLN C 230 " pdb=" C GLN C 230 " pdb=" N PRO C 231 " pdb=" CA PRO C 231 " ideal model delta harmonic sigma weight residual -180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 ... (remaining 12425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2326 0.061 - 0.122: 685 0.122 - 0.183: 94 0.183 - 0.243: 16 0.243 - 0.304: 17 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CG LEU C 574 " pdb=" CB LEU C 574 " pdb=" CD1 LEU C 574 " pdb=" CD2 LEU C 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU B 574 " pdb=" CB LEU B 574 " pdb=" CD1 LEU B 574 " pdb=" CD2 LEU B 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU A 574 " pdb=" CB LEU A 574 " pdb=" CD1 LEU A 574 " pdb=" CD2 LEU A 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 3135 not shown) Planarity restraints: 3522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO C 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO D 354 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 353 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO B 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " 0.035 5.00e-02 4.00e+02 ... (remaining 3519 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5727 2.81 - 3.33: 18721 3.33 - 3.85: 32002 3.85 - 4.38: 37526 4.38 - 4.90: 59416 Nonbonded interactions: 153392 Sorted by model distance: nonbonded pdb=" O MET B 578 " pdb=" OG1 THR B 581 " model vdw 2.286 3.040 nonbonded pdb=" O MET C 578 " pdb=" OG1 THR C 581 " model vdw 2.286 3.040 nonbonded pdb=" O MET A 578 " pdb=" OG1 THR A 581 " model vdw 2.287 3.040 nonbonded pdb=" O MET D 578 " pdb=" OG1 THR D 581 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.311 3.040 ... (remaining 153387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 19 through 701) selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.280 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.209 20602 Z= 0.431 Angle : 1.076 13.788 27945 Z= 0.545 Chirality : 0.059 0.304 3138 Planarity : 0.007 0.064 3522 Dihedral : 11.498 112.584 7740 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.56 % Allowed : 6.68 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.12), residues: 2472 helix: -3.35 (0.09), residues: 1224 sheet: -4.24 (0.42), residues: 76 loop : -3.09 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 385 TYR 0.014 0.002 TYR D 623 PHE 0.015 0.002 PHE A 523 TRP 0.022 0.002 TRP C 629 HIS 0.007 0.002 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00871 (20602) covalent geometry : angle 1.07563 (27945) hydrogen bonds : bond 0.30857 ( 780) hydrogen bonds : angle 9.07503 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1064 time to evaluate : 0.767 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: 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 70 CYS cc_start: 0.7566 (p) cc_final: 0.7277 (p) REVERT: A 113 GLU cc_start: 0.9357 (tt0) cc_final: 0.8968 (tm-30) REVERT: A 122 HIS cc_start: 0.9451 (m170) cc_final: 0.9147 (m-70) REVERT: A 123 ILE cc_start: 0.9671 (mt) cc_final: 0.9287 (mt) REVERT: A 136 LEU cc_start: 0.9461 (mt) cc_final: 0.9182 (mt) REVERT: A 146 ARG cc_start: 0.9320 (mtt180) cc_final: 0.8860 (mmm-85) REVERT: A 150 THR cc_start: 0.9184 (p) cc_final: 0.8694 (p) REVERT: A 198 THR cc_start: 0.9662 (t) cc_final: 0.9121 (t) REVERT: A 201 HIS cc_start: 0.9368 (m-70) cc_final: 0.8824 (m90) REVERT: A 215 MET cc_start: 0.9168 (mmm) cc_final: 0.8920 (mmm) REVERT: A 250 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 259 LEU cc_start: 0.9376 (mm) cc_final: 0.9070 (mm) REVERT: A 260 MET cc_start: 0.9593 (tpt) cc_final: 0.9280 (mmm) REVERT: A 263 ARG cc_start: 0.9493 (mmt180) cc_final: 0.9206 (mmp80) REVERT: A 297 ILE cc_start: 0.9309 (pp) cc_final: 0.9004 (tp) REVERT: A 300 LYS cc_start: 0.9002 (mttt) cc_final: 0.8559 (mppt) REVERT: A 306 GLN cc_start: 0.9102 (pt0) cc_final: 0.8680 (pm20) REVERT: A 336 TYR cc_start: 0.9036 (t80) cc_final: 0.8540 (t80) REVERT: A 347 CYS cc_start: 0.9382 (m) cc_final: 0.8345 (m) REVERT: A 403 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8895 (tp30) REVERT: A 406 ASP cc_start: 0.9326 (m-30) cc_final: 0.9114 (m-30) REVERT: A 410 MET cc_start: 0.8936 (mmm) cc_final: 0.8692 (tpp) REVERT: A 421 LEU cc_start: 0.9429 (tm) cc_final: 0.8942 (tm) REVERT: A 440 MET cc_start: 0.9039 (ppp) cc_final: 0.8684 (mmm) REVERT: A 442 MET cc_start: 0.8323 (mtt) cc_final: 0.7901 (tmm) REVERT: A 454 MET cc_start: 0.9251 (mtt) cc_final: 0.8932 (mmt) REVERT: A 458 LEU cc_start: 0.9803 (mm) cc_final: 0.9428 (mm) REVERT: A 463 CYS cc_start: 0.9483 (m) cc_final: 0.9249 (m) REVERT: A 465 VAL cc_start: 0.9607 (t) cc_final: 0.9237 (t) REVERT: A 478 PHE cc_start: 0.9643 (t80) cc_final: 0.9434 (t80) REVERT: A 483 GLN cc_start: 0.9693 (tt0) cc_final: 0.9314 (tp40) REVERT: A 494 CYS cc_start: 0.9114 (t) cc_final: 0.8845 (p) REVERT: A 497 MET cc_start: 0.9432 (ttp) cc_final: 0.8915 (ttp) REVERT: A 536 LEU cc_start: 0.9752 (mt) cc_final: 0.9542 (mt) REVERT: A 551 LEU cc_start: 0.8026 (mt) cc_final: 0.7542 (mp) REVERT: A 587 HIS cc_start: 0.8997 (p90) cc_final: 0.8259 (p-80) REVERT: A 588 GLU cc_start: 0.9505 (pt0) cc_final: 0.9023 (pp20) REVERT: A 591 GLU cc_start: 0.9052 (pp20) cc_final: 0.8758 (pm20) REVERT: B 57 ASP cc_start: 0.8941 (m-30) cc_final: 0.8524 (m-30) REVERT: B 70 CYS cc_start: 0.8414 (p) cc_final: 0.8051 (p) REVERT: B 78 MET cc_start: 0.8202 (ptp) cc_final: 0.7927 (ptp) REVERT: B 88 LEU cc_start: 0.9418 (tt) cc_final: 0.9191 (tt) REVERT: B 99 MET cc_start: 0.9311 (mtm) cc_final: 0.8779 (tpp) REVERT: B 113 GLU cc_start: 0.9541 (tt0) cc_final: 0.9149 (tm-30) REVERT: B 118 GLN cc_start: 0.9243 (tt0) cc_final: 0.8910 (tm-30) REVERT: B 123 ILE cc_start: 0.9373 (mt) cc_final: 0.9089 (mt) REVERT: B 128 GLN cc_start: 0.9107 (pt0) cc_final: 0.8444 (tm-30) REVERT: B 150 THR cc_start: 0.9385 (p) cc_final: 0.8954 (p) REVERT: B 169 PHE cc_start: 0.9099 (m-10) cc_final: 0.8816 (m-80) REVERT: B 200 LEU cc_start: 0.9654 (mm) cc_final: 0.9388 (mt) REVERT: B 204 ILE cc_start: 0.9590 (mt) cc_final: 0.9277 (tp) REVERT: B 234 LEU cc_start: 0.9008 (mm) cc_final: 0.8298 (mt) REVERT: B 246 LEU cc_start: 0.9616 (tp) cc_final: 0.9355 (tp) REVERT: B 294 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8823 (mt-10) REVERT: B 300 LYS cc_start: 0.9012 (mttt) cc_final: 0.8573 (mppt) REVERT: B 460 LEU cc_start: 0.9308 (mm) cc_final: 0.9024 (mm) REVERT: B 463 CYS cc_start: 0.9475 (m) cc_final: 0.9149 (m) REVERT: B 464 ASN cc_start: 0.9376 (m-40) cc_final: 0.8948 (m-40) REVERT: B 478 PHE cc_start: 0.9640 (t80) cc_final: 0.9338 (t80) REVERT: B 483 GLN cc_start: 0.9723 (tt0) cc_final: 0.9389 (tp40) REVERT: B 497 MET cc_start: 0.9427 (ttp) cc_final: 0.9003 (ttp) REVERT: B 518 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9033 (pp20) REVERT: B 526 TYR cc_start: 0.8916 (t80) cc_final: 0.8628 (t80) REVERT: B 551 LEU cc_start: 0.9311 (mt) cc_final: 0.8974 (mp) REVERT: B 605 GLU cc_start: 0.9169 (tt0) cc_final: 0.8886 (tt0) REVERT: B 627 ASP cc_start: 0.9275 (m-30) cc_final: 0.9048 (t0) REVERT: C 35 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8870 (mp0) REVERT: C 39 LEU cc_start: 0.9582 (tp) cc_final: 0.9313 (tp) REVERT: C 42 LYS cc_start: 0.9378 (tttt) cc_final: 0.9091 (pttt) REVERT: C 83 LEU cc_start: 0.9756 (tp) cc_final: 0.9513 (tp) REVERT: C 84 HIS cc_start: 0.9110 (m90) cc_final: 0.8273 (m170) REVERT: C 93 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8942 (pm20) REVERT: C 96 MET cc_start: 0.9251 (mmt) cc_final: 0.9011 (mmm) REVERT: C 99 MET cc_start: 0.8940 (mtm) cc_final: 0.8531 (ptp) REVERT: C 113 GLU cc_start: 0.9384 (tt0) cc_final: 0.9095 (tm-30) REVERT: C 136 LEU cc_start: 0.9393 (mt) cc_final: 0.9113 (mt) REVERT: C 161 TYR cc_start: 0.9071 (t80) cc_final: 0.8737 (t80) REVERT: C 184 GLU cc_start: 0.9317 (pt0) cc_final: 0.8954 (tm-30) REVERT: C 200 LEU cc_start: 0.9572 (mm) cc_final: 0.9122 (mt) REVERT: C 204 ILE cc_start: 0.9577 (mt) cc_final: 0.9299 (mt) REVERT: C 246 LEU cc_start: 0.9702 (tp) cc_final: 0.9444 (tp) REVERT: C 260 MET cc_start: 0.9675 (tpt) cc_final: 0.9445 (mmm) REVERT: C 263 ARG cc_start: 0.9619 (mmt180) cc_final: 0.9404 (mmm-85) REVERT: C 297 ILE cc_start: 0.9416 (pp) cc_final: 0.9056 (tp) REVERT: C 300 LYS cc_start: 0.9044 (mttt) cc_final: 0.8533 (mppt) REVERT: C 303 GLU cc_start: 0.9303 (pt0) cc_final: 0.8784 (pp20) REVERT: C 306 GLN cc_start: 0.9104 (pt0) cc_final: 0.8604 (pm20) REVERT: C 327 PRO cc_start: 0.9194 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: C 343 PHE cc_start: 0.9660 (t80) cc_final: 0.9458 (t80) REVERT: C 347 CYS cc_start: 0.9155 (m) cc_final: 0.8894 (m) REVERT: C 367 LEU cc_start: 0.9613 (tt) cc_final: 0.9358 (tp) REVERT: C 403 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9095 (tp30) REVERT: C 421 LEU cc_start: 0.9443 (tm) cc_final: 0.9053 (tm) REVERT: C 463 CYS cc_start: 0.9331 (m) cc_final: 0.9088 (m) REVERT: C 478 PHE cc_start: 0.9609 (t80) cc_final: 0.9309 (t80) REVERT: C 494 CYS cc_start: 0.9113 (t) cc_final: 0.8735 (p) REVERT: C 497 MET cc_start: 0.9549 (ttp) cc_final: 0.9161 (tmm) REVERT: C 536 LEU cc_start: 0.9754 (mt) cc_final: 0.9543 (mt) REVERT: C 538 LEU cc_start: 0.9640 (mp) cc_final: 0.9434 (mp) REVERT: C 541 ILE cc_start: 0.9303 (pt) cc_final: 0.9081 (pt) REVERT: C 577 MET cc_start: 0.9199 (ptm) cc_final: 0.8562 (ppp) REVERT: D 35 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 49 LEU cc_start: 0.9402 (pt) cc_final: 0.9093 (mp) REVERT: D 84 HIS cc_start: 0.9157 (m90) cc_final: 0.8407 (m-70) REVERT: D 93 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9029 (pm20) REVERT: D 99 MET cc_start: 0.9032 (mtm) cc_final: 0.8738 (ptp) REVERT: D 113 GLU cc_start: 0.9413 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 122 HIS cc_start: 0.9522 (m170) cc_final: 0.9298 (m-70) REVERT: D 136 LEU cc_start: 0.9457 (mt) cc_final: 0.9166 (mt) REVERT: D 161 TYR cc_start: 0.8891 (t80) cc_final: 0.8616 (t80) REVERT: D 200 LEU cc_start: 0.9518 (mm) cc_final: 0.9023 (mt) REVERT: D 204 ILE cc_start: 0.9573 (mt) cc_final: 0.9262 (mt) REVERT: D 209 LYS cc_start: 0.8623 (mttt) cc_final: 0.7822 (mttt) REVERT: D 246 LEU cc_start: 0.9690 (tp) cc_final: 0.9407 (tp) REVERT: D 250 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 259 LEU cc_start: 0.9480 (mm) cc_final: 0.9120 (mm) REVERT: D 260 MET cc_start: 0.9635 (tpt) cc_final: 0.9392 (mmm) REVERT: D 300 LYS cc_start: 0.8877 (mttt) cc_final: 0.8387 (mppt) REVERT: D 306 GLN cc_start: 0.9139 (pt0) cc_final: 0.8472 (mp10) REVERT: D 336 TYR cc_start: 0.9183 (t80) cc_final: 0.8861 (t80) REVERT: D 343 PHE cc_start: 0.9745 (t80) cc_final: 0.9411 (t80) REVERT: D 347 CYS cc_start: 0.9335 (m) cc_final: 0.8900 (m) REVERT: D 367 LEU cc_start: 0.9621 (tt) cc_final: 0.9269 (tt) REVERT: D 403 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8851 (tp30) REVERT: D 410 MET cc_start: 0.9048 (mmm) cc_final: 0.8798 (tmm) REVERT: D 418 GLN cc_start: 0.9518 (tp40) cc_final: 0.9291 (mp10) REVERT: D 463 CYS cc_start: 0.9384 (m) cc_final: 0.9104 (m) REVERT: D 478 PHE cc_start: 0.9586 (t80) cc_final: 0.9328 (t80) REVERT: D 483 GLN cc_start: 0.9704 (tt0) cc_final: 0.9426 (mm-40) REVERT: D 494 CYS cc_start: 0.9167 (t) cc_final: 0.8779 (p) REVERT: D 536 LEU cc_start: 0.9772 (mt) cc_final: 0.9533 (mt) REVERT: D 537 PHE cc_start: 0.9435 (t80) cc_final: 0.9231 (t80) REVERT: D 538 LEU cc_start: 0.9601 (mp) cc_final: 0.9400 (mp) REVERT: D 541 ILE cc_start: 0.9197 (pt) cc_final: 0.8869 (pt) REVERT: D 577 MET cc_start: 0.9243 (ptm) cc_final: 0.8618 (ppp) outliers start: 12 outliers final: 8 residues processed: 1065 average time/residue: 0.1318 time to fit residues: 219.0070 Evaluate side-chains 740 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 732 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 118 GLN A 201 HIS A 217 ASN A 239 GLN A 572 ASN A 582 HIS A 596 GLN B 74 GLN B 91 ASN B 118 GLN B 201 HIS B 239 GLN B 265 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 596 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 265 HIS C 572 ASN C 582 HIS C 596 GLN C 637 GLN D 74 GLN D 201 HIS D 217 ASN D 596 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057942 restraints weight = 61506.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.061017 restraints weight = 32642.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.063404 restraints weight = 21126.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.065191 restraints weight = 15255.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.066410 restraints weight = 11691.686| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20602 Z= 0.187 Angle : 0.769 9.564 27945 Z= 0.400 Chirality : 0.046 0.208 3138 Planarity : 0.006 0.069 3522 Dihedral : 7.579 108.427 2928 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.09 % Allowed : 4.08 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.16), residues: 2472 helix: -1.32 (0.13), residues: 1348 sheet: -4.10 (0.55), residues: 48 loop : -2.77 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 146 TYR 0.017 0.002 TYR C 526 PHE 0.024 0.002 PHE C 211 TRP 0.013 0.002 TRP B 629 HIS 0.011 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00383 (20602) covalent geometry : angle 0.76889 (27945) hydrogen bonds : bond 0.05935 ( 780) hydrogen bonds : angle 5.40361 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 925 time to evaluate : 0.705 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 113 GLU cc_start: 0.9303 (tt0) cc_final: 0.9048 (tm-30) REVERT: A 146 ARG cc_start: 0.9379 (mtt180) cc_final: 0.8869 (mmm-85) REVERT: A 215 MET cc_start: 0.9470 (mmm) cc_final: 0.8996 (mmm) REVERT: A 245 LYS cc_start: 0.8464 (mttt) cc_final: 0.8067 (mtpt) REVERT: A 255 MET cc_start: 0.9383 (mmp) cc_final: 0.8938 (tpp) REVERT: A 263 ARG cc_start: 0.9310 (mmt180) cc_final: 0.9088 (mmp80) REVERT: A 300 LYS cc_start: 0.8948 (mttt) cc_final: 0.8531 (mppt) REVERT: A 301 LYS cc_start: 0.9295 (tptp) cc_final: 0.9017 (tptt) REVERT: A 306 GLN cc_start: 0.8963 (pt0) cc_final: 0.8511 (mp10) REVERT: A 336 TYR cc_start: 0.9162 (t80) cc_final: 0.8899 (t80) REVERT: A 403 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8888 (tp30) REVERT: A 421 LEU cc_start: 0.9036 (tt) cc_final: 0.8669 (pp) REVERT: A 437 LEU cc_start: 0.9617 (mm) cc_final: 0.9332 (mp) REVERT: A 440 MET cc_start: 0.9118 (ppp) cc_final: 0.8843 (tpt) REVERT: A 454 MET cc_start: 0.9309 (mtt) cc_final: 0.8945 (mmt) REVERT: A 465 VAL cc_start: 0.9572 (t) cc_final: 0.9344 (t) REVERT: A 466 MET cc_start: 0.9732 (mtt) cc_final: 0.9370 (mmm) REVERT: A 483 GLN cc_start: 0.9713 (tt0) cc_final: 0.9376 (tp40) REVERT: A 497 MET cc_start: 0.9458 (ttp) cc_final: 0.8789 (ttp) REVERT: A 537 PHE cc_start: 0.9563 (t80) cc_final: 0.8484 (t80) REVERT: A 538 LEU cc_start: 0.9402 (mp) cc_final: 0.9105 (mp) REVERT: A 551 LEU cc_start: 0.8037 (mt) cc_final: 0.7709 (mp) REVERT: A 569 LEU cc_start: 0.9823 (tp) cc_final: 0.9605 (tp) REVERT: A 580 ASP cc_start: 0.8640 (m-30) cc_final: 0.8214 (m-30) REVERT: A 605 GLU cc_start: 0.9306 (tt0) cc_final: 0.9015 (mt-10) REVERT: B 93 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8972 (pm20) REVERT: B 96 MET cc_start: 0.9598 (mmt) cc_final: 0.9321 (mmm) REVERT: B 99 MET cc_start: 0.9388 (mtm) cc_final: 0.8751 (tpp) REVERT: B 113 GLU cc_start: 0.9507 (tt0) cc_final: 0.9140 (tm-30) REVERT: B 118 GLN cc_start: 0.9354 (tt0) cc_final: 0.8848 (tp40) REVERT: B 123 ILE cc_start: 0.9519 (mt) cc_final: 0.9171 (mt) REVERT: B 128 GLN cc_start: 0.9120 (pt0) cc_final: 0.8414 (tm-30) REVERT: B 174 ASN cc_start: 0.8912 (t0) cc_final: 0.8433 (t0) REVERT: B 182 LEU cc_start: 0.9724 (mm) cc_final: 0.9472 (mm) REVERT: B 204 ILE cc_start: 0.9526 (mt) cc_final: 0.9274 (mt) REVERT: B 209 LYS cc_start: 0.9341 (mttt) cc_final: 0.8805 (ttmt) REVERT: B 219 LEU cc_start: 0.9759 (mt) cc_final: 0.9413 (mm) REVERT: B 246 LEU cc_start: 0.9637 (tp) cc_final: 0.9314 (tp) REVERT: B 259 LEU cc_start: 0.9732 (mm) cc_final: 0.9474 (mm) REVERT: B 260 MET cc_start: 0.9608 (mmm) cc_final: 0.9187 (mmm) REVERT: B 294 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8795 (mt-10) REVERT: B 297 ILE cc_start: 0.9522 (pt) cc_final: 0.9249 (tp) REVERT: B 300 LYS cc_start: 0.8901 (mttt) cc_final: 0.8482 (mppt) REVERT: B 306 GLN cc_start: 0.8927 (pt0) cc_final: 0.8448 (mp10) REVERT: B 372 LEU cc_start: 0.9388 (pp) cc_final: 0.8872 (tt) REVERT: B 403 GLU cc_start: 0.8937 (tp30) cc_final: 0.8723 (tp30) REVERT: B 410 MET cc_start: 0.9044 (tmm) cc_final: 0.8571 (tmm) REVERT: B 421 LEU cc_start: 0.9211 (tt) cc_final: 0.8786 (tt) REVERT: B 454 MET cc_start: 0.9536 (mmt) cc_final: 0.8882 (tpp) REVERT: B 463 CYS cc_start: 0.9366 (m) cc_final: 0.9152 (m) REVERT: B 483 GLN cc_start: 0.9706 (tt0) cc_final: 0.9427 (mm-40) REVERT: B 494 CYS cc_start: 0.8901 (t) cc_final: 0.8695 (p) REVERT: B 497 MET cc_start: 0.9302 (ttp) cc_final: 0.8768 (ttp) REVERT: B 526 TYR cc_start: 0.9015 (t80) cc_final: 0.8752 (t80) REVERT: B 528 MET cc_start: 0.8289 (mmp) cc_final: 0.7976 (tpp) REVERT: B 537 PHE cc_start: 0.9374 (t80) cc_final: 0.8324 (t80) REVERT: B 538 LEU cc_start: 0.9137 (mp) cc_final: 0.8647 (mp) REVERT: B 568 LEU cc_start: 0.9531 (tp) cc_final: 0.9324 (tp) REVERT: B 570 MET cc_start: 0.9279 (mmp) cc_final: 0.9034 (mmm) REVERT: B 592 LEU cc_start: 0.9431 (mm) cc_final: 0.9202 (mm) REVERT: C 35 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8919 (mp0) REVERT: C 84 HIS cc_start: 0.9201 (m90) cc_final: 0.8875 (m90) REVERT: C 93 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8894 (pm20) REVERT: C 96 MET cc_start: 0.9318 (mmt) cc_final: 0.8714 (tmm) REVERT: C 99 MET cc_start: 0.9039 (mtm) cc_final: 0.8563 (ptp) REVERT: C 113 GLU cc_start: 0.9456 (tt0) cc_final: 0.9216 (tm-30) REVERT: C 137 LEU cc_start: 0.9693 (mm) cc_final: 0.9432 (pp) REVERT: C 204 ILE cc_start: 0.9551 (mt) cc_final: 0.9255 (mt) REVERT: C 209 LYS cc_start: 0.8879 (mttt) cc_final: 0.8304 (ttmt) REVERT: C 215 MET cc_start: 0.9387 (mmp) cc_final: 0.8970 (mmm) REVERT: C 245 LYS cc_start: 0.8890 (mttt) cc_final: 0.8479 (ptpp) REVERT: C 259 LEU cc_start: 0.9635 (mm) cc_final: 0.9422 (mm) REVERT: C 260 MET cc_start: 0.9670 (tpt) cc_final: 0.9384 (mmm) REVERT: C 263 ARG cc_start: 0.9600 (mmt180) cc_final: 0.9399 (mmm-85) REVERT: C 294 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8661 (mt-10) REVERT: C 300 LYS cc_start: 0.8860 (mttt) cc_final: 0.8390 (mppt) REVERT: C 301 LYS cc_start: 0.8869 (tttt) cc_final: 0.8090 (ttpt) REVERT: C 303 GLU cc_start: 0.9228 (pt0) cc_final: 0.8853 (pp20) REVERT: C 306 GLN cc_start: 0.8970 (pt0) cc_final: 0.8653 (pm20) REVERT: C 343 PHE cc_start: 0.9527 (t80) cc_final: 0.9216 (t80) REVERT: C 347 CYS cc_start: 0.8888 (m) cc_final: 0.8602 (m) REVERT: C 403 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8975 (tp30) REVERT: C 410 MET cc_start: 0.9240 (tmm) cc_final: 0.8681 (tmm) REVERT: C 454 MET cc_start: 0.9523 (mmt) cc_final: 0.9192 (tpp) REVERT: C 463 CYS cc_start: 0.9255 (m) cc_final: 0.8871 (m) REVERT: C 483 GLN cc_start: 0.9696 (tt0) cc_final: 0.9370 (mm-40) REVERT: C 485 MET cc_start: 0.9777 (mtp) cc_final: 0.9428 (mmm) REVERT: C 494 CYS cc_start: 0.9024 (t) cc_final: 0.8775 (p) REVERT: C 497 MET cc_start: 0.9384 (ttp) cc_final: 0.9025 (tmm) REVERT: C 538 LEU cc_start: 0.9384 (mp) cc_final: 0.9066 (mp) REVERT: C 593 TRP cc_start: 0.9204 (t60) cc_final: 0.8743 (t60) REVERT: D 35 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8853 (mt-10) REVERT: D 39 LEU cc_start: 0.9513 (tp) cc_final: 0.9221 (tp) REVERT: D 84 HIS cc_start: 0.9217 (m90) cc_final: 0.8651 (m170) REVERT: D 93 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9038 (pm20) REVERT: D 96 MET cc_start: 0.9271 (mmp) cc_final: 0.8869 (mmm) REVERT: D 99 MET cc_start: 0.9090 (mtm) cc_final: 0.8714 (ptp) REVERT: D 113 GLU cc_start: 0.9556 (tt0) cc_final: 0.9264 (tm-30) REVERT: D 122 HIS cc_start: 0.9569 (m170) cc_final: 0.9315 (m170) REVERT: D 136 LEU cc_start: 0.9407 (mt) cc_final: 0.8998 (mt) REVERT: D 159 LEU cc_start: 0.8806 (mm) cc_final: 0.8601 (mm) REVERT: D 198 THR cc_start: 0.9638 (t) cc_final: 0.9438 (m) REVERT: D 204 ILE cc_start: 0.9519 (mt) cc_final: 0.9218 (mt) REVERT: D 209 LYS cc_start: 0.8605 (mttt) cc_final: 0.8220 (mtpt) REVERT: D 215 MET cc_start: 0.9424 (mmp) cc_final: 0.8998 (mmm) REVERT: D 245 LYS cc_start: 0.8753 (mttt) cc_final: 0.8122 (ptpp) REVERT: D 246 LEU cc_start: 0.9749 (tp) cc_final: 0.9522 (tp) REVERT: D 250 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 260 MET cc_start: 0.9640 (tpt) cc_final: 0.9317 (mmm) REVERT: D 292 LEU cc_start: 0.9500 (tt) cc_final: 0.9044 (mp) REVERT: D 300 LYS cc_start: 0.8861 (mttt) cc_final: 0.8384 (mppt) REVERT: D 306 GLN cc_start: 0.8884 (pt0) cc_final: 0.8608 (mp10) REVERT: D 372 LEU cc_start: 0.9146 (pp) cc_final: 0.8476 (pp) REVERT: D 403 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8882 (tp30) REVERT: D 437 LEU cc_start: 0.9439 (mm) cc_final: 0.9202 (mp) REVERT: D 440 MET cc_start: 0.8217 (mmm) cc_final: 0.7866 (mmm) REVERT: D 454 MET cc_start: 0.9489 (mmt) cc_final: 0.9189 (mmt) REVERT: D 483 GLN cc_start: 0.9708 (tt0) cc_final: 0.9427 (mm-40) REVERT: D 494 CYS cc_start: 0.9171 (t) cc_final: 0.8878 (p) REVERT: D 536 LEU cc_start: 0.9752 (mt) cc_final: 0.9532 (mt) REVERT: D 538 LEU cc_start: 0.9437 (mp) cc_final: 0.8974 (mp) REVERT: D 542 ASP cc_start: 0.7457 (t0) cc_final: 0.6676 (t0) REVERT: D 569 LEU cc_start: 0.9805 (tp) cc_final: 0.9595 (tp) REVERT: D 593 TRP cc_start: 0.9170 (t60) cc_final: 0.8900 (t60) outliers start: 2 outliers final: 0 residues processed: 925 average time/residue: 0.1271 time to fit residues: 187.4993 Evaluate side-chains 691 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 691 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 224 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 267 GLN A 582 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN D 118 GLN D 572 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058129 restraints weight = 61485.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.061225 restraints weight = 32903.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.063573 restraints weight = 21475.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065328 restraints weight = 15470.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066675 restraints weight = 11917.670| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20602 Z= 0.150 Angle : 0.716 8.644 27945 Z= 0.363 Chirality : 0.045 0.213 3138 Planarity : 0.005 0.063 3522 Dihedral : 6.935 101.086 2928 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.96 % 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 are not related in a simple way. whole: -2.38 (0.16), residues: 2472 helix: -0.74 (0.13), residues: 1364 sheet: -4.01 (0.57), residues: 48 loop : -2.58 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 385 TYR 0.015 0.001 TYR C 526 PHE 0.014 0.001 PHE D 468 TRP 0.012 0.001 TRP B 613 HIS 0.009 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00304 (20602) covalent geometry : angle 0.71607 (27945) hydrogen bonds : bond 0.05232 ( 780) hydrogen bonds : angle 5.06805 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 845 time to evaluate : 0.780 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: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8742 (mt-10) REVERT: A 39 LEU cc_start: 0.9543 (tp) cc_final: 0.9130 (tp) REVERT: A 42 LYS cc_start: 0.9369 (tttt) cc_final: 0.8994 (pttm) REVERT: A 93 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9120 (pm20) REVERT: A 113 GLU cc_start: 0.9498 (tt0) cc_final: 0.9030 (tm-30) REVERT: A 146 ARG cc_start: 0.9388 (mtt180) cc_final: 0.8915 (mmm-85) REVERT: A 150 THR cc_start: 0.9126 (t) cc_final: 0.8875 (t) REVERT: A 215 MET cc_start: 0.9478 (mmm) cc_final: 0.9020 (mmm) REVERT: A 245 LYS cc_start: 0.8429 (mttt) cc_final: 0.7954 (mtpp) REVERT: A 260 MET cc_start: 0.9642 (tpt) cc_final: 0.9318 (mmm) REVERT: A 297 ILE cc_start: 0.9513 (mm) cc_final: 0.9175 (tp) REVERT: A 300 LYS cc_start: 0.8980 (mttt) cc_final: 0.8464 (mppt) REVERT: A 306 GLN cc_start: 0.8911 (pt0) cc_final: 0.8640 (pm20) REVERT: A 399 ILE cc_start: 0.9238 (mt) cc_final: 0.8795 (mt) REVERT: A 403 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8868 (tp30) REVERT: A 410 MET cc_start: 0.9256 (tpt) cc_final: 0.8610 (tpp) REVERT: A 421 LEU cc_start: 0.8994 (tt) cc_final: 0.8743 (pp) REVERT: A 440 MET cc_start: 0.9090 (ppp) cc_final: 0.8788 (mmm) REVERT: A 454 MET cc_start: 0.9286 (mtt) cc_final: 0.8946 (mmm) REVERT: A 466 MET cc_start: 0.9725 (mtt) cc_final: 0.9482 (mtt) REVERT: A 483 GLN cc_start: 0.9695 (tt0) cc_final: 0.9370 (tp40) REVERT: A 497 MET cc_start: 0.9355 (ttp) cc_final: 0.8844 (ttp) REVERT: A 515 GLU cc_start: 0.9131 (tp30) cc_final: 0.8701 (tp30) REVERT: A 537 PHE cc_start: 0.9589 (t80) cc_final: 0.8511 (t80) REVERT: A 538 LEU cc_start: 0.9278 (mp) cc_final: 0.9028 (mp) REVERT: A 551 LEU cc_start: 0.8098 (mt) cc_final: 0.7876 (mp) REVERT: A 570 MET cc_start: 0.9278 (mmp) cc_final: 0.8965 (mmm) REVERT: A 580 ASP cc_start: 0.8650 (m-30) cc_final: 0.8118 (m-30) REVERT: B 50 LEU cc_start: 0.9147 (mp) cc_final: 0.8512 (tp) REVERT: B 70 CYS cc_start: 0.8638 (p) cc_final: 0.7921 (p) REVERT: B 93 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8973 (pm20) REVERT: B 96 MET cc_start: 0.9585 (mmt) cc_final: 0.9291 (mmm) REVERT: B 99 MET cc_start: 0.9422 (mtm) cc_final: 0.8791 (tpp) REVERT: B 113 GLU cc_start: 0.9505 (tt0) cc_final: 0.9153 (tm-30) REVERT: B 118 GLN cc_start: 0.9430 (tt0) cc_final: 0.8952 (tm-30) REVERT: B 123 ILE cc_start: 0.9567 (mt) cc_final: 0.9190 (mt) REVERT: B 128 GLN cc_start: 0.9099 (pt0) cc_final: 0.8337 (tm-30) REVERT: B 174 ASN cc_start: 0.8961 (t0) cc_final: 0.8684 (t0) REVERT: B 201 HIS cc_start: 0.9501 (m90) cc_final: 0.9139 (m90) REVERT: B 204 ILE cc_start: 0.9535 (mt) cc_final: 0.9306 (mt) REVERT: B 209 LYS cc_start: 0.9242 (mttt) cc_final: 0.8653 (ttmt) REVERT: B 245 LYS cc_start: 0.9332 (mttt) cc_final: 0.8981 (ptpp) REVERT: B 246 LEU cc_start: 0.9624 (tp) cc_final: 0.9417 (tp) REVERT: B 260 MET cc_start: 0.9590 (mmm) cc_final: 0.9127 (mmm) REVERT: B 293 LEU cc_start: 0.9761 (mt) cc_final: 0.9478 (pp) REVERT: B 294 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8433 (mt-10) REVERT: B 300 LYS cc_start: 0.8917 (mttt) cc_final: 0.8492 (mppt) REVERT: B 306 GLN cc_start: 0.8892 (pt0) cc_final: 0.8546 (mp10) REVERT: B 403 GLU cc_start: 0.8990 (tp30) cc_final: 0.8724 (tp30) REVERT: B 454 MET cc_start: 0.9558 (mmt) cc_final: 0.8865 (tpp) REVERT: B 463 CYS cc_start: 0.9322 (m) cc_final: 0.9015 (m) REVERT: B 483 GLN cc_start: 0.9693 (tt0) cc_final: 0.9417 (tp40) REVERT: B 494 CYS cc_start: 0.8934 (t) cc_final: 0.8719 (p) REVERT: B 497 MET cc_start: 0.9309 (ttp) cc_final: 0.8738 (ttp) REVERT: B 528 MET cc_start: 0.8227 (mmp) cc_final: 0.7859 (tpp) REVERT: B 537 PHE cc_start: 0.9450 (t80) cc_final: 0.8286 (t80) REVERT: B 538 LEU cc_start: 0.9107 (mp) cc_final: 0.8539 (mp) REVERT: B 568 LEU cc_start: 0.9498 (tp) cc_final: 0.9296 (tp) REVERT: C 35 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8918 (mt-10) REVERT: C 84 HIS cc_start: 0.9185 (m90) cc_final: 0.8751 (m90) REVERT: C 93 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8938 (pm20) REVERT: C 96 MET cc_start: 0.9330 (mmt) cc_final: 0.8930 (mmm) REVERT: C 137 LEU cc_start: 0.9690 (mm) cc_final: 0.9461 (pp) REVERT: C 198 THR cc_start: 0.9677 (t) cc_final: 0.9460 (m) REVERT: C 204 ILE cc_start: 0.9586 (mt) cc_final: 0.9287 (mt) REVERT: C 206 GLN cc_start: 0.9298 (mm-40) cc_final: 0.8819 (mm110) REVERT: C 209 LYS cc_start: 0.8839 (mttt) cc_final: 0.8168 (ttmt) REVERT: C 215 MET cc_start: 0.9365 (mmp) cc_final: 0.8952 (mmm) REVERT: C 245 LYS cc_start: 0.8895 (mttt) cc_final: 0.8342 (ptpp) REVERT: C 246 LEU cc_start: 0.9696 (tp) cc_final: 0.9449 (tp) REVERT: C 250 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8701 (mm-30) REVERT: C 255 MET cc_start: 0.9423 (tpp) cc_final: 0.9217 (tpp) REVERT: C 260 MET cc_start: 0.9680 (tpt) cc_final: 0.9371 (mmm) REVERT: C 262 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9191 (ttmm) REVERT: C 263 ARG cc_start: 0.9605 (mmt180) cc_final: 0.9294 (mmp80) REVERT: C 300 LYS cc_start: 0.9019 (mttt) cc_final: 0.8545 (mppt) REVERT: C 301 LYS cc_start: 0.8793 (tttt) cc_final: 0.8352 (ttpt) REVERT: C 303 GLU cc_start: 0.9164 (pt0) cc_final: 0.8872 (pp20) REVERT: C 306 GLN cc_start: 0.8980 (pt0) cc_final: 0.8667 (pm20) REVERT: C 343 PHE cc_start: 0.9544 (t80) cc_final: 0.9331 (t80) REVERT: C 403 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8928 (tp30) REVERT: C 454 MET cc_start: 0.9574 (mmt) cc_final: 0.9336 (mmt) REVERT: C 485 MET cc_start: 0.9730 (mtp) cc_final: 0.9421 (mmm) REVERT: C 497 MET cc_start: 0.9435 (ttp) cc_final: 0.8785 (tmm) REVERT: C 537 PHE cc_start: 0.9551 (t80) cc_final: 0.9264 (t80) REVERT: C 538 LEU cc_start: 0.9230 (mp) cc_final: 0.8850 (mp) REVERT: C 570 MET cc_start: 0.9271 (mmp) cc_final: 0.9054 (mmm) REVERT: C 577 MET cc_start: 0.9000 (ppp) cc_final: 0.8797 (ppp) REVERT: C 593 TRP cc_start: 0.9231 (t60) cc_final: 0.8851 (t60) REVERT: D 35 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8853 (mt-10) REVERT: D 84 HIS cc_start: 0.9095 (m90) cc_final: 0.8811 (m90) REVERT: D 93 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9014 (pm20) REVERT: D 96 MET cc_start: 0.9291 (mmp) cc_final: 0.8798 (mmp) REVERT: D 99 MET cc_start: 0.9100 (mtm) cc_final: 0.8787 (ptp) REVERT: D 113 GLU cc_start: 0.9564 (tt0) cc_final: 0.9261 (tm-30) REVERT: D 136 LEU cc_start: 0.9441 (mt) cc_final: 0.8994 (mt) REVERT: D 198 THR cc_start: 0.9625 (t) cc_final: 0.9413 (m) REVERT: D 204 ILE cc_start: 0.9568 (mt) cc_final: 0.9291 (mt) REVERT: D 205 LEU cc_start: 0.8991 (pp) cc_final: 0.8785 (pp) REVERT: D 206 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8725 (mm110) REVERT: D 209 LYS cc_start: 0.8736 (mttt) cc_final: 0.8202 (mtpt) REVERT: D 215 MET cc_start: 0.9398 (mmp) cc_final: 0.8972 (mmm) REVERT: D 245 LYS cc_start: 0.8766 (mttt) cc_final: 0.8210 (ptpp) REVERT: D 246 LEU cc_start: 0.9746 (tp) cc_final: 0.9508 (tp) REVERT: D 250 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8419 (mm-30) REVERT: D 255 MET cc_start: 0.9488 (tpp) cc_final: 0.9260 (tpp) REVERT: D 260 MET cc_start: 0.9645 (tpt) cc_final: 0.9317 (mmm) REVERT: D 300 LYS cc_start: 0.8894 (mttt) cc_final: 0.8425 (mppt) REVERT: D 303 GLU cc_start: 0.9184 (tp30) cc_final: 0.8757 (tp30) REVERT: D 306 GLN cc_start: 0.8871 (pt0) cc_final: 0.8605 (pm20) REVERT: D 343 PHE cc_start: 0.9514 (t80) cc_final: 0.9314 (t80) REVERT: D 367 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8904 (tp) REVERT: D 399 ILE cc_start: 0.8364 (mm) cc_final: 0.8120 (mm) REVERT: D 403 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8798 (tp30) REVERT: D 410 MET cc_start: 0.9251 (tpt) cc_final: 0.8541 (tpp) REVERT: D 421 LEU cc_start: 0.9292 (tp) cc_final: 0.8804 (tp) REVERT: D 440 MET cc_start: 0.8250 (mmm) cc_final: 0.7801 (mmm) REVERT: D 454 MET cc_start: 0.9384 (mmt) cc_final: 0.9136 (mmt) REVERT: D 463 CYS cc_start: 0.9283 (m) cc_final: 0.9064 (m) REVERT: D 483 GLN cc_start: 0.9717 (tt0) cc_final: 0.9424 (tp40) REVERT: D 485 MET cc_start: 0.9762 (mtp) cc_final: 0.9438 (mmm) REVERT: D 494 CYS cc_start: 0.9123 (t) cc_final: 0.8830 (p) REVERT: D 497 MET cc_start: 0.8935 (tmm) cc_final: 0.8732 (tmm) REVERT: D 536 LEU cc_start: 0.9763 (mt) cc_final: 0.9552 (mt) REVERT: D 538 LEU cc_start: 0.9221 (mp) cc_final: 0.9014 (mp) REVERT: D 570 MET cc_start: 0.9254 (mmp) cc_final: 0.8943 (mmm) REVERT: D 593 TRP cc_start: 0.9170 (t60) cc_final: 0.8944 (t60) outliers start: 2 outliers final: 0 residues processed: 845 average time/residue: 0.1235 time to fit residues: 168.2058 Evaluate side-chains 673 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 74 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.056973 restraints weight = 62348.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.059964 restraints weight = 33523.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062364 restraints weight = 21907.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064069 restraints weight = 15819.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065383 restraints weight = 12266.771| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20602 Z= 0.152 Angle : 0.710 10.589 27945 Z= 0.359 Chirality : 0.045 0.199 3138 Planarity : 0.005 0.059 3522 Dihedral : 6.529 93.573 2928 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 are not related in a simple way. whole: -2.08 (0.17), residues: 2472 helix: -0.41 (0.14), residues: 1380 sheet: -4.05 (0.56), residues: 48 loop : -2.61 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.016 0.001 TYR B 161 PHE 0.017 0.001 PHE D 537 TRP 0.011 0.001 TRP A 268 HIS 0.012 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00308 (20602) covalent geometry : angle 0.71029 (27945) hydrogen bonds : bond 0.04481 ( 780) hydrogen bonds : angle 4.85995 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 830 time to evaluate : 0.659 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 35 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 39 LEU cc_start: 0.9581 (tp) cc_final: 0.9227 (tp) REVERT: A 42 LYS cc_start: 0.9348 (tttt) cc_final: 0.8984 (pttm) REVERT: A 113 GLU cc_start: 0.9509 (tt0) cc_final: 0.9021 (tm-30) REVERT: A 123 ILE cc_start: 0.9660 (mm) cc_final: 0.9447 (tt) REVERT: A 146 ARG cc_start: 0.9424 (mtt180) cc_final: 0.8924 (mmm-85) REVERT: A 150 THR cc_start: 0.9145 (t) cc_final: 0.8880 (t) REVERT: A 178 ILE cc_start: 0.9665 (mp) cc_final: 0.9430 (mp) REVERT: A 182 LEU cc_start: 0.9700 (mm) cc_final: 0.9490 (mm) REVERT: A 206 GLN cc_start: 0.9371 (mm-40) cc_final: 0.8813 (mm110) REVERT: A 215 MET cc_start: 0.9451 (mmm) cc_final: 0.9031 (mmm) REVERT: A 245 LYS cc_start: 0.8536 (mttt) cc_final: 0.7943 (mtpp) REVERT: A 255 MET cc_start: 0.9342 (mmm) cc_final: 0.9007 (tpp) REVERT: A 260 MET cc_start: 0.9652 (tpt) cc_final: 0.9312 (mmm) REVERT: A 297 ILE cc_start: 0.9519 (mm) cc_final: 0.9299 (tp) REVERT: A 300 LYS cc_start: 0.9021 (mttt) cc_final: 0.8508 (mppt) REVERT: A 301 LYS cc_start: 0.9374 (tptt) cc_final: 0.9059 (tmtt) REVERT: A 306 GLN cc_start: 0.8890 (pt0) cc_final: 0.8613 (pm20) REVERT: A 399 ILE cc_start: 0.9233 (mt) cc_final: 0.8822 (mt) REVERT: A 403 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8884 (tp30) REVERT: A 410 MET cc_start: 0.9205 (tpt) cc_final: 0.8225 (tpp) REVERT: A 440 MET cc_start: 0.9077 (ppp) cc_final: 0.8854 (tpt) REVERT: A 454 MET cc_start: 0.9282 (mtt) cc_final: 0.9000 (mmm) REVERT: A 483 GLN cc_start: 0.9680 (tt0) cc_final: 0.9337 (tp-100) REVERT: A 497 MET cc_start: 0.9392 (ttp) cc_final: 0.8893 (ttp) REVERT: A 518 GLU cc_start: 0.9243 (mp0) cc_final: 0.9012 (mp0) REVERT: A 537 PHE cc_start: 0.9602 (t80) cc_final: 0.8575 (t80) REVERT: A 538 LEU cc_start: 0.9234 (mp) cc_final: 0.9019 (mp) REVERT: A 541 ILE cc_start: 0.8684 (pt) cc_final: 0.8275 (mm) REVERT: A 551 LEU cc_start: 0.8203 (mt) cc_final: 0.7991 (mp) REVERT: A 570 MET cc_start: 0.9386 (mmp) cc_final: 0.9073 (mmm) REVERT: A 580 ASP cc_start: 0.8929 (m-30) cc_final: 0.8430 (m-30) REVERT: A 605 GLU cc_start: 0.9346 (tt0) cc_final: 0.9072 (tt0) REVERT: B 57 ASP cc_start: 0.9219 (m-30) cc_final: 0.8810 (m-30) REVERT: B 70 CYS cc_start: 0.8693 (p) cc_final: 0.8180 (p) REVERT: B 93 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8990 (pm20) REVERT: B 96 MET cc_start: 0.9592 (mmt) cc_final: 0.9289 (mmm) REVERT: B 113 GLU cc_start: 0.9488 (tt0) cc_final: 0.9115 (tm-30) REVERT: B 118 GLN cc_start: 0.9412 (tt0) cc_final: 0.8980 (tm-30) REVERT: B 209 LYS cc_start: 0.9215 (mttt) cc_final: 0.8645 (ttmt) REVERT: B 245 LYS cc_start: 0.9320 (mttt) cc_final: 0.8803 (ptpp) REVERT: B 260 MET cc_start: 0.9596 (mmm) cc_final: 0.9126 (mmm) REVERT: B 293 LEU cc_start: 0.9763 (mt) cc_final: 0.9477 (pp) REVERT: B 294 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 300 LYS cc_start: 0.8930 (mttt) cc_final: 0.8392 (mppt) REVERT: B 303 GLU cc_start: 0.9066 (tp30) cc_final: 0.8483 (tp30) REVERT: B 306 GLN cc_start: 0.8950 (pt0) cc_final: 0.8497 (pm20) REVERT: B 421 LEU cc_start: 0.9364 (tp) cc_final: 0.8880 (tp) REVERT: B 454 MET cc_start: 0.9538 (mmt) cc_final: 0.8881 (tpp) REVERT: B 463 CYS cc_start: 0.9339 (m) cc_final: 0.9106 (m) REVERT: B 483 GLN cc_start: 0.9686 (tt0) cc_final: 0.9329 (tp40) REVERT: B 491 MET cc_start: 0.8840 (ttt) cc_final: 0.8543 (ttt) REVERT: B 497 MET cc_start: 0.9347 (ttp) cc_final: 0.8703 (ttp) REVERT: B 528 MET cc_start: 0.8225 (mmp) cc_final: 0.7404 (mmm) REVERT: B 537 PHE cc_start: 0.9471 (t80) cc_final: 0.8348 (t80) REVERT: B 538 LEU cc_start: 0.9096 (mp) cc_final: 0.8804 (mp) REVERT: B 541 ILE cc_start: 0.8930 (pt) cc_final: 0.8702 (pt) REVERT: B 570 MET cc_start: 0.9463 (mmm) cc_final: 0.9188 (mmm) REVERT: B 589 ARG cc_start: 0.9271 (ptt90) cc_final: 0.9066 (ptm-80) REVERT: C 35 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8931 (mt-10) REVERT: C 42 LYS cc_start: 0.9305 (tttt) cc_final: 0.9105 (pttm) REVERT: C 93 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8954 (pm20) REVERT: C 96 MET cc_start: 0.9325 (mmt) cc_final: 0.8954 (mmm) REVERT: C 110 MET cc_start: 0.9189 (mmm) cc_final: 0.8856 (mmm) REVERT: C 137 LEU cc_start: 0.9687 (mm) cc_final: 0.9466 (pp) REVERT: C 204 ILE cc_start: 0.9609 (mt) cc_final: 0.9328 (mt) REVERT: C 206 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8670 (mm-40) REVERT: C 209 LYS cc_start: 0.8798 (mttt) cc_final: 0.8149 (ttmt) REVERT: C 215 MET cc_start: 0.9364 (mmp) cc_final: 0.9030 (mmm) REVERT: C 230 GLN cc_start: 0.8525 (mt0) cc_final: 0.8241 (mt0) REVERT: C 245 LYS cc_start: 0.8966 (mttt) cc_final: 0.8418 (ptpp) REVERT: C 246 LEU cc_start: 0.9708 (tp) cc_final: 0.9471 (tp) REVERT: C 250 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8717 (mm-30) REVERT: C 259 LEU cc_start: 0.9673 (mm) cc_final: 0.9445 (mm) REVERT: C 260 MET cc_start: 0.9676 (tpt) cc_final: 0.9378 (mmm) REVERT: C 263 ARG cc_start: 0.9619 (mmt180) cc_final: 0.9373 (mmm-85) REVERT: C 300 LYS cc_start: 0.9017 (mttt) cc_final: 0.8556 (mppt) REVERT: C 301 LYS cc_start: 0.8752 (tttt) cc_final: 0.8269 (ttpt) REVERT: C 303 GLU cc_start: 0.9158 (pt0) cc_final: 0.8845 (pp20) REVERT: C 306 GLN cc_start: 0.9019 (pt0) cc_final: 0.8697 (pm20) REVERT: C 343 PHE cc_start: 0.9580 (t80) cc_final: 0.9358 (t80) REVERT: C 403 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8908 (tp30) REVERT: C 485 MET cc_start: 0.9709 (mtp) cc_final: 0.9485 (mmm) REVERT: C 497 MET cc_start: 0.9247 (ttp) cc_final: 0.8678 (tmm) REVERT: C 537 PHE cc_start: 0.9532 (t80) cc_final: 0.9243 (t80) REVERT: C 538 LEU cc_start: 0.9196 (mp) cc_final: 0.8838 (mp) REVERT: C 570 MET cc_start: 0.9377 (mmp) cc_final: 0.9141 (mmm) REVERT: C 593 TRP cc_start: 0.9225 (t60) cc_final: 0.8861 (t60) REVERT: D 35 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8885 (mt-10) REVERT: D 84 HIS cc_start: 0.9146 (m90) cc_final: 0.8771 (m90) REVERT: D 93 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8993 (pm20) REVERT: D 96 MET cc_start: 0.9368 (mmp) cc_final: 0.8910 (mmp) REVERT: D 99 MET cc_start: 0.9112 (mtm) cc_final: 0.8807 (ptp) REVERT: D 113 GLU cc_start: 0.9549 (tt0) cc_final: 0.9259 (tm-30) REVERT: D 123 ILE cc_start: 0.9692 (tt) cc_final: 0.9464 (mp) REVERT: D 161 TYR cc_start: 0.8811 (t80) cc_final: 0.8359 (t80) REVERT: D 204 ILE cc_start: 0.9607 (mt) cc_final: 0.9357 (mt) REVERT: D 206 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8792 (mm-40) REVERT: D 209 LYS cc_start: 0.8653 (mttt) cc_final: 0.8213 (mtpt) REVERT: D 215 MET cc_start: 0.9390 (mmp) cc_final: 0.8912 (mmm) REVERT: D 245 LYS cc_start: 0.8788 (mttt) cc_final: 0.8251 (ptpp) REVERT: D 246 LEU cc_start: 0.9724 (tp) cc_final: 0.9489 (tp) REVERT: D 250 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8377 (mm-30) REVERT: D 255 MET cc_start: 0.9514 (tpp) cc_final: 0.9313 (tpp) REVERT: D 260 MET cc_start: 0.9669 (tpt) cc_final: 0.9331 (mmm) REVERT: D 300 LYS cc_start: 0.8904 (mttt) cc_final: 0.8476 (mppt) REVERT: D 301 LYS cc_start: 0.9369 (tptt) cc_final: 0.9161 (tptt) REVERT: D 303 GLU cc_start: 0.9140 (tp30) cc_final: 0.8717 (mm-30) REVERT: D 343 PHE cc_start: 0.9545 (t80) cc_final: 0.9288 (t80) REVERT: D 347 CYS cc_start: 0.8636 (m) cc_final: 0.8323 (m) REVERT: D 403 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8787 (tp30) REVERT: D 410 MET cc_start: 0.9273 (tpt) cc_final: 0.8596 (tpp) REVERT: D 463 CYS cc_start: 0.9392 (m) cc_final: 0.9055 (m) REVERT: D 485 MET cc_start: 0.9735 (mtp) cc_final: 0.9510 (mmm) REVERT: D 497 MET cc_start: 0.8952 (tmm) cc_final: 0.8643 (tmm) REVERT: D 536 LEU cc_start: 0.9763 (mt) cc_final: 0.9509 (mt) REVERT: D 570 MET cc_start: 0.9285 (mmp) cc_final: 0.9001 (mmm) REVERT: D 593 TRP cc_start: 0.9144 (t60) cc_final: 0.8485 (t60) outliers start: 0 outliers final: 0 residues processed: 830 average time/residue: 0.1227 time to fit residues: 164.1177 Evaluate side-chains 684 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 186 optimal weight: 0.0370 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.056311 restraints weight = 63297.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.059223 restraints weight = 34330.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.061660 restraints weight = 22518.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.063366 restraints weight = 16093.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.064578 restraints weight = 12527.913| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20602 Z= 0.162 Angle : 0.712 8.589 27945 Z= 0.361 Chirality : 0.045 0.206 3138 Planarity : 0.004 0.058 3522 Dihedral : 6.257 86.244 2928 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.10 % 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 are not related in a simple way. whole: -2.06 (0.17), residues: 2472 helix: -0.36 (0.14), residues: 1388 sheet: -4.06 (0.55), residues: 48 loop : -2.65 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 43 TYR 0.016 0.001 TYR C 526 PHE 0.016 0.001 PHE B 553 TRP 0.008 0.001 TRP B 629 HIS 0.012 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00332 (20602) covalent geometry : angle 0.71205 (27945) hydrogen bonds : bond 0.04260 ( 780) hydrogen bonds : angle 4.85164 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 796 time to evaluate : 0.746 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 35 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8790 (mt-10) REVERT: A 39 LEU cc_start: 0.9618 (tp) cc_final: 0.9207 (tp) REVERT: A 42 LYS cc_start: 0.9348 (tttt) cc_final: 0.9001 (pttt) REVERT: A 113 GLU cc_start: 0.9536 (tt0) cc_final: 0.9012 (tm-30) REVERT: A 146 ARG cc_start: 0.9468 (mtt180) cc_final: 0.8993 (mmm-85) REVERT: A 150 THR cc_start: 0.9213 (t) cc_final: 0.8908 (t) REVERT: A 206 GLN cc_start: 0.9361 (mm-40) cc_final: 0.8948 (mm110) REVERT: A 209 LYS cc_start: 0.8368 (mttt) cc_final: 0.8062 (ttmt) REVERT: A 215 MET cc_start: 0.9428 (mmm) cc_final: 0.8990 (mmm) REVERT: A 250 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8790 (mm-30) REVERT: A 260 MET cc_start: 0.9660 (tpt) cc_final: 0.9347 (mmm) REVERT: A 297 ILE cc_start: 0.9447 (mm) cc_final: 0.9227 (tp) REVERT: A 300 LYS cc_start: 0.9075 (mttt) cc_final: 0.8563 (mppt) REVERT: A 306 GLN cc_start: 0.8944 (pt0) cc_final: 0.8667 (mp10) REVERT: A 403 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8876 (tp30) REVERT: A 410 MET cc_start: 0.9020 (tpt) cc_final: 0.8210 (tpp) REVERT: A 418 GLN cc_start: 0.9486 (mp10) cc_final: 0.9197 (pm20) REVERT: A 454 MET cc_start: 0.9311 (mtt) cc_final: 0.9032 (mmm) REVERT: A 463 CYS cc_start: 0.9335 (m) cc_final: 0.9105 (m) REVERT: A 483 GLN cc_start: 0.9659 (tt0) cc_final: 0.9374 (tt0) REVERT: A 497 MET cc_start: 0.9398 (ttp) cc_final: 0.8954 (ttp) REVERT: A 515 GLU cc_start: 0.9152 (tp30) cc_final: 0.8682 (tp30) REVERT: A 518 GLU cc_start: 0.9301 (mp0) cc_final: 0.9073 (mp0) REVERT: A 537 PHE cc_start: 0.9611 (t80) cc_final: 0.8648 (t80) REVERT: A 538 LEU cc_start: 0.9236 (mp) cc_final: 0.9036 (mp) REVERT: A 541 ILE cc_start: 0.8735 (pt) cc_final: 0.8387 (mm) REVERT: A 570 MET cc_start: 0.9459 (mmp) cc_final: 0.9106 (mmm) REVERT: A 605 GLU cc_start: 0.9380 (tt0) cc_final: 0.9088 (tt0) REVERT: B 57 ASP cc_start: 0.9150 (m-30) cc_final: 0.8741 (m-30) REVERT: B 70 CYS cc_start: 0.8419 (p) cc_final: 0.7906 (p) REVERT: B 93 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8980 (pm20) REVERT: B 96 MET cc_start: 0.9606 (mmt) cc_final: 0.9274 (mmm) REVERT: B 99 MET cc_start: 0.9395 (mtm) cc_final: 0.8728 (tpp) REVERT: B 110 MET cc_start: 0.9045 (mmm) cc_final: 0.8617 (mmm) REVERT: B 113 GLU cc_start: 0.9496 (tt0) cc_final: 0.9134 (tm-30) REVERT: B 118 GLN cc_start: 0.9465 (tt0) cc_final: 0.9062 (tm-30) REVERT: B 123 ILE cc_start: 0.9577 (mt) cc_final: 0.9224 (mt) REVERT: B 128 GLN cc_start: 0.9177 (pt0) cc_final: 0.8310 (tm-30) REVERT: B 209 LYS cc_start: 0.9184 (mttt) cc_final: 0.8620 (ttmt) REVERT: B 245 LYS cc_start: 0.9246 (mttt) cc_final: 0.8741 (ptpp) REVERT: B 246 LEU cc_start: 0.9715 (tp) cc_final: 0.9492 (tp) REVERT: B 260 MET cc_start: 0.9596 (mmm) cc_final: 0.9070 (mmm) REVERT: B 293 LEU cc_start: 0.9763 (mt) cc_final: 0.9493 (pp) REVERT: B 294 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8555 (mt-10) REVERT: B 300 LYS cc_start: 0.8920 (mttt) cc_final: 0.8395 (mppt) REVERT: B 301 LYS cc_start: 0.8452 (tmtt) cc_final: 0.8222 (tmtt) REVERT: B 303 GLU cc_start: 0.9090 (tp30) cc_final: 0.8496 (tp30) REVERT: B 306 GLN cc_start: 0.8980 (pt0) cc_final: 0.8538 (pm20) REVERT: B 403 GLU cc_start: 0.9056 (tp30) cc_final: 0.8703 (tp30) REVERT: B 421 LEU cc_start: 0.9224 (tp) cc_final: 0.8976 (tp) REVERT: B 454 MET cc_start: 0.9447 (mmt) cc_final: 0.8798 (tpp) REVERT: B 463 CYS cc_start: 0.9409 (m) cc_final: 0.9184 (m) REVERT: B 483 GLN cc_start: 0.9678 (tt0) cc_final: 0.9326 (tp40) REVERT: B 497 MET cc_start: 0.9248 (ttp) cc_final: 0.8762 (ttp) REVERT: B 518 GLU cc_start: 0.9057 (mp0) cc_final: 0.8805 (mp0) REVERT: B 528 MET cc_start: 0.8240 (mmp) cc_final: 0.7354 (mmm) REVERT: B 537 PHE cc_start: 0.9486 (t80) cc_final: 0.8425 (t80) REVERT: B 538 LEU cc_start: 0.9128 (mp) cc_final: 0.8879 (mp) REVERT: B 541 ILE cc_start: 0.9062 (pt) cc_final: 0.8832 (pt) REVERT: C 34 ASP cc_start: 0.9547 (m-30) cc_final: 0.9280 (m-30) REVERT: C 35 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8868 (mt-10) REVERT: C 42 LYS cc_start: 0.9255 (tttt) cc_final: 0.9032 (pttm) REVERT: C 93 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8819 (pm20) REVERT: C 96 MET cc_start: 0.9319 (mmt) cc_final: 0.8907 (tmm) REVERT: C 110 MET cc_start: 0.9188 (mmm) cc_final: 0.8936 (mmm) REVERT: C 137 LEU cc_start: 0.9688 (mm) cc_final: 0.9454 (pp) REVERT: C 204 ILE cc_start: 0.9622 (mt) cc_final: 0.9371 (mt) REVERT: C 206 GLN cc_start: 0.9347 (mm-40) cc_final: 0.8754 (mm-40) REVERT: C 209 LYS cc_start: 0.8885 (mttt) cc_final: 0.8236 (ttmt) REVERT: C 215 MET cc_start: 0.9383 (mmp) cc_final: 0.8936 (mmm) REVERT: C 245 LYS cc_start: 0.8958 (mttt) cc_final: 0.8449 (ptpp) REVERT: C 246 LEU cc_start: 0.9721 (tp) cc_final: 0.9473 (tp) REVERT: C 250 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8496 (mm-30) REVERT: C 260 MET cc_start: 0.9676 (tpt) cc_final: 0.9377 (mmm) REVERT: C 300 LYS cc_start: 0.9028 (mttt) cc_final: 0.8604 (mppt) REVERT: C 306 GLN cc_start: 0.9044 (pt0) cc_final: 0.8470 (pm20) REVERT: C 343 PHE cc_start: 0.9574 (t80) cc_final: 0.9358 (t80) REVERT: C 403 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8901 (tp30) REVERT: C 410 MET cc_start: 0.9018 (tmm) cc_final: 0.8710 (tmm) REVERT: C 450 GLU cc_start: 0.9546 (pm20) cc_final: 0.9183 (pm20) REVERT: C 454 MET cc_start: 0.9454 (mmt) cc_final: 0.8980 (tpp) REVERT: C 483 GLN cc_start: 0.9694 (tt0) cc_final: 0.9428 (tt0) REVERT: C 497 MET cc_start: 0.9232 (ttp) cc_final: 0.8609 (tmm) REVERT: C 518 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8977 (tm-30) REVERT: C 537 PHE cc_start: 0.9521 (t80) cc_final: 0.9191 (t80) REVERT: C 570 MET cc_start: 0.9421 (mmp) cc_final: 0.9119 (mmm) REVERT: C 593 TRP cc_start: 0.9224 (t60) cc_final: 0.8837 (t60) REVERT: D 35 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8912 (mt-10) REVERT: D 93 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8949 (pm20) REVERT: D 96 MET cc_start: 0.9406 (mmp) cc_final: 0.8930 (mmp) REVERT: D 99 MET cc_start: 0.9095 (mtm) cc_final: 0.8813 (ptp) REVERT: D 113 GLU cc_start: 0.9578 (tt0) cc_final: 0.9289 (tm-30) REVERT: D 204 ILE cc_start: 0.9627 (mt) cc_final: 0.9366 (mt) REVERT: D 209 LYS cc_start: 0.8641 (mttt) cc_final: 0.8243 (mtpt) REVERT: D 215 MET cc_start: 0.9353 (mmp) cc_final: 0.8896 (mmm) REVERT: D 245 LYS cc_start: 0.8713 (mttt) cc_final: 0.8315 (ptpp) REVERT: D 246 LEU cc_start: 0.9719 (tp) cc_final: 0.9481 (tp) REVERT: D 250 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8357 (mm-30) REVERT: D 260 MET cc_start: 0.9685 (tpt) cc_final: 0.9344 (mmm) REVERT: D 300 LYS cc_start: 0.8973 (mttt) cc_final: 0.8546 (mppt) REVERT: D 303 GLU cc_start: 0.9211 (tp30) cc_final: 0.8997 (tp30) REVERT: D 367 LEU cc_start: 0.9325 (tp) cc_final: 0.9049 (tp) REVERT: D 403 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8811 (tp30) REVERT: D 410 MET cc_start: 0.9285 (tpt) cc_final: 0.8590 (tpp) REVERT: D 442 MET cc_start: 0.9507 (ptm) cc_final: 0.9145 (ppp) REVERT: D 483 GLN cc_start: 0.9719 (tt0) cc_final: 0.9414 (tp40) REVERT: D 570 MET cc_start: 0.9371 (mmp) cc_final: 0.9053 (mmm) REVERT: D 593 TRP cc_start: 0.9197 (t60) cc_final: 0.8576 (t60) REVERT: D 600 THR cc_start: 0.9752 (t) cc_final: 0.9503 (p) REVERT: D 605 GLU cc_start: 0.9289 (tt0) cc_final: 0.9047 (tt0) outliers start: 1 outliers final: 0 residues processed: 797 average time/residue: 0.1212 time to fit residues: 155.3631 Evaluate side-chains 658 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.056105 restraints weight = 63388.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059029 restraints weight = 34352.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.061173 restraints weight = 22659.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.062911 restraints weight = 16501.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.064185 restraints weight = 12910.726| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20602 Z= 0.141 Angle : 0.700 7.453 27945 Z= 0.351 Chirality : 0.045 0.165 3138 Planarity : 0.004 0.058 3522 Dihedral : 5.885 71.808 2928 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % 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 are not related in a simple way. whole: -1.87 (0.17), residues: 2472 helix: -0.19 (0.14), residues: 1388 sheet: -3.59 (0.43), residues: 64 loop : -2.58 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.019 0.001 TYR B 161 PHE 0.029 0.001 PHE A 508 TRP 0.009 0.001 TRP A 268 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00294 (20602) covalent geometry : angle 0.70022 (27945) hydrogen bonds : bond 0.04042 ( 780) hydrogen bonds : angle 4.73832 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 781 time to evaluate : 0.767 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: A 35 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8766 (mt-10) REVERT: A 39 LEU cc_start: 0.9562 (tp) cc_final: 0.9225 (tp) REVERT: A 42 LYS cc_start: 0.9330 (tttt) cc_final: 0.9001 (pttt) REVERT: A 84 HIS cc_start: 0.8931 (m170) cc_final: 0.8696 (m170) REVERT: A 113 GLU cc_start: 0.9553 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 150 THR cc_start: 0.9218 (t) cc_final: 0.8931 (t) REVERT: A 206 GLN cc_start: 0.9438 (mm-40) cc_final: 0.8942 (mm110) REVERT: A 209 LYS cc_start: 0.8658 (mttt) cc_final: 0.8224 (ttmt) REVERT: A 215 MET cc_start: 0.9415 (mmm) cc_final: 0.8977 (mmm) REVERT: A 245 LYS cc_start: 0.8659 (mttt) cc_final: 0.8030 (mtpp) REVERT: A 260 MET cc_start: 0.9658 (tpt) cc_final: 0.9364 (mmm) REVERT: A 282 GLU cc_start: 0.9002 (mp0) cc_final: 0.8752 (mm-30) REVERT: A 300 LYS cc_start: 0.9072 (mttt) cc_final: 0.8578 (mppt) REVERT: A 301 LYS cc_start: 0.9353 (tptt) cc_final: 0.8912 (tmtt) REVERT: A 306 GLN cc_start: 0.8888 (pt0) cc_final: 0.8622 (mp10) REVERT: A 343 PHE cc_start: 0.9639 (t80) cc_final: 0.9382 (t80) REVERT: A 399 ILE cc_start: 0.9228 (mt) cc_final: 0.8965 (mt) REVERT: A 403 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8848 (tp30) REVERT: A 410 MET cc_start: 0.8975 (tpt) cc_final: 0.8220 (tpp) REVERT: A 418 GLN cc_start: 0.9538 (mp10) cc_final: 0.9297 (pm20) REVERT: A 435 MET cc_start: 0.8853 (mmt) cc_final: 0.8638 (mmp) REVERT: A 440 MET cc_start: 0.8611 (tpt) cc_final: 0.8235 (tpp) REVERT: A 454 MET cc_start: 0.9309 (mtt) cc_final: 0.8732 (tpp) REVERT: A 463 CYS cc_start: 0.9376 (m) cc_final: 0.9175 (m) REVERT: A 483 GLN cc_start: 0.9633 (tt0) cc_final: 0.9338 (tt0) REVERT: A 497 MET cc_start: 0.9411 (ttp) cc_final: 0.8971 (ttp) REVERT: A 518 GLU cc_start: 0.9352 (mp0) cc_final: 0.9109 (mp0) REVERT: A 526 TYR cc_start: 0.8711 (t80) cc_final: 0.8255 (t80) REVERT: A 537 PHE cc_start: 0.9600 (t80) cc_final: 0.8715 (t80) REVERT: A 570 MET cc_start: 0.9536 (mmp) cc_final: 0.9157 (mmm) REVERT: A 605 GLU cc_start: 0.9392 (tt0) cc_final: 0.9114 (tt0) REVERT: B 57 ASP cc_start: 0.9080 (m-30) cc_final: 0.8696 (m-30) REVERT: B 70 CYS cc_start: 0.8411 (p) cc_final: 0.7905 (p) REVERT: B 96 MET cc_start: 0.9611 (mmt) cc_final: 0.9291 (mmm) REVERT: B 99 MET cc_start: 0.9381 (mtm) cc_final: 0.8695 (tpp) REVERT: B 113 GLU cc_start: 0.9488 (tt0) cc_final: 0.9092 (tm-30) REVERT: B 118 GLN cc_start: 0.9486 (tt0) cc_final: 0.9072 (tm-30) REVERT: B 123 ILE cc_start: 0.9568 (mt) cc_final: 0.9216 (mt) REVERT: B 128 GLN cc_start: 0.9131 (pt0) cc_final: 0.8235 (tm-30) REVERT: B 206 GLN cc_start: 0.9550 (mm-40) cc_final: 0.8808 (mm110) REVERT: B 209 LYS cc_start: 0.9166 (mttt) cc_final: 0.8604 (ttmt) REVERT: B 245 LYS cc_start: 0.9217 (mttt) cc_final: 0.8707 (ptpp) REVERT: B 260 MET cc_start: 0.9595 (mmm) cc_final: 0.9113 (mmm) REVERT: B 293 LEU cc_start: 0.9759 (mt) cc_final: 0.9505 (pp) REVERT: B 294 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 300 LYS cc_start: 0.8982 (mttt) cc_final: 0.8451 (mppt) REVERT: B 301 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8206 (tmtt) REVERT: B 306 GLN cc_start: 0.8987 (pt0) cc_final: 0.8650 (mp10) REVERT: B 347 CYS cc_start: 0.8777 (p) cc_final: 0.8531 (p) REVERT: B 403 GLU cc_start: 0.9084 (tp30) cc_final: 0.8858 (tp30) REVERT: B 421 LEU cc_start: 0.9299 (tp) cc_final: 0.9087 (tp) REVERT: B 440 MET cc_start: 0.9396 (tpp) cc_final: 0.9099 (tpp) REVERT: B 454 MET cc_start: 0.9412 (mmt) cc_final: 0.8702 (tpp) REVERT: B 463 CYS cc_start: 0.9417 (m) cc_final: 0.9150 (m) REVERT: B 483 GLN cc_start: 0.9665 (tt0) cc_final: 0.9294 (tp40) REVERT: B 497 MET cc_start: 0.9316 (ttp) cc_final: 0.8834 (ttp) REVERT: B 528 MET cc_start: 0.8170 (mmp) cc_final: 0.7714 (tpp) REVERT: B 537 PHE cc_start: 0.9451 (t80) cc_final: 0.8465 (t80) REVERT: B 541 ILE cc_start: 0.9077 (pt) cc_final: 0.8849 (pt) REVERT: C 35 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8923 (mt-10) REVERT: C 42 LYS cc_start: 0.9329 (tttt) cc_final: 0.9094 (pttm) REVERT: C 93 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8788 (pm20) REVERT: C 96 MET cc_start: 0.9312 (mmt) cc_final: 0.8935 (tmm) REVERT: C 110 MET cc_start: 0.9153 (mmm) cc_final: 0.8921 (mmm) REVERT: C 137 LEU cc_start: 0.9679 (mm) cc_final: 0.9457 (pp) REVERT: C 204 ILE cc_start: 0.9586 (mt) cc_final: 0.9341 (mt) REVERT: C 206 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8732 (mm-40) REVERT: C 209 LYS cc_start: 0.8836 (mttt) cc_final: 0.8276 (ttmt) REVERT: C 215 MET cc_start: 0.9385 (mmp) cc_final: 0.8921 (mmm) REVERT: C 245 LYS cc_start: 0.8978 (mttt) cc_final: 0.8426 (ptpp) REVERT: C 246 LEU cc_start: 0.9712 (tp) cc_final: 0.9466 (tp) REVERT: C 250 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8562 (mm-30) REVERT: C 259 LEU cc_start: 0.9583 (mm) cc_final: 0.9379 (mm) REVERT: C 260 MET cc_start: 0.9690 (tpt) cc_final: 0.9357 (mmm) REVERT: C 300 LYS cc_start: 0.9094 (mttt) cc_final: 0.8601 (mppt) REVERT: C 301 LYS cc_start: 0.9348 (tptp) cc_final: 0.8904 (tmtt) REVERT: C 306 GLN cc_start: 0.8917 (pt0) cc_final: 0.8636 (mp10) REVERT: C 403 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8896 (tp30) REVERT: C 454 MET cc_start: 0.9429 (mmt) cc_final: 0.9156 (tpp) REVERT: C 483 GLN cc_start: 0.9674 (tt0) cc_final: 0.9455 (tt0) REVERT: C 497 MET cc_start: 0.9228 (ttp) cc_final: 0.8770 (ttp) REVERT: C 518 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8962 (tm-30) REVERT: C 537 PHE cc_start: 0.9521 (t80) cc_final: 0.8851 (t80) REVERT: C 538 LEU cc_start: 0.9214 (mp) cc_final: 0.8821 (mp) REVERT: C 541 ILE cc_start: 0.9155 (mm) cc_final: 0.8846 (mm) REVERT: C 570 MET cc_start: 0.9458 (mmp) cc_final: 0.9184 (mmm) REVERT: C 593 TRP cc_start: 0.9180 (t60) cc_final: 0.8882 (t60) REVERT: D 35 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8875 (mt-10) REVERT: D 93 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8890 (pm20) REVERT: D 96 MET cc_start: 0.9412 (mmp) cc_final: 0.8900 (mmm) REVERT: D 99 MET cc_start: 0.9109 (mtm) cc_final: 0.8751 (ptp) REVERT: D 113 GLU cc_start: 0.9581 (tt0) cc_final: 0.9289 (tm-30) REVERT: D 204 ILE cc_start: 0.9595 (mt) cc_final: 0.9357 (mt) REVERT: D 206 GLN cc_start: 0.9381 (mm-40) cc_final: 0.8805 (mm-40) REVERT: D 209 LYS cc_start: 0.8658 (mttt) cc_final: 0.8312 (mtpt) REVERT: D 215 MET cc_start: 0.9354 (mmp) cc_final: 0.8897 (mmm) REVERT: D 245 LYS cc_start: 0.8785 (mttt) cc_final: 0.8274 (ptpp) REVERT: D 246 LEU cc_start: 0.9717 (tp) cc_final: 0.9478 (tp) REVERT: D 250 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 260 MET cc_start: 0.9696 (tpt) cc_final: 0.9324 (mmm) REVERT: D 300 LYS cc_start: 0.8975 (mttt) cc_final: 0.8458 (mppt) REVERT: D 301 LYS cc_start: 0.9383 (tptt) cc_final: 0.8603 (tmtt) REVERT: D 403 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8803 (tp30) REVERT: D 410 MET cc_start: 0.9287 (tpt) cc_final: 0.9072 (mmm) REVERT: D 442 MET cc_start: 0.9471 (ptm) cc_final: 0.9105 (ppp) REVERT: D 483 GLN cc_start: 0.9735 (tt0) cc_final: 0.9412 (tp40) REVERT: D 515 GLU cc_start: 0.9088 (tp30) cc_final: 0.8529 (tp30) REVERT: D 536 LEU cc_start: 0.9735 (mt) cc_final: 0.9508 (mt) REVERT: D 570 MET cc_start: 0.9456 (mmp) cc_final: 0.9107 (mmm) REVERT: D 593 TRP cc_start: 0.9169 (t60) cc_final: 0.8581 (t60) REVERT: D 605 GLU cc_start: 0.9307 (tt0) cc_final: 0.9086 (tt0) outliers start: 1 outliers final: 0 residues processed: 782 average time/residue: 0.1193 time to fit residues: 150.1986 Evaluate side-chains 655 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 93 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 136 optimal weight: 0.0020 chunk 232 optimal weight: 0.2980 chunk 238 optimal weight: 0.0970 chunk 215 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 40 optimal weight: 0.0040 overall best weight: 0.0856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 464 ASN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 74 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059091 restraints weight = 60922.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062102 restraints weight = 33163.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.064418 restraints weight = 21772.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066124 restraints weight = 15914.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067498 restraints weight = 12347.163| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20602 Z= 0.131 Angle : 0.706 7.169 27945 Z= 0.346 Chirality : 0.044 0.157 3138 Planarity : 0.004 0.059 3522 Dihedral : 5.282 49.917 2928 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 are not related in a simple way. whole: -1.64 (0.17), residues: 2472 helix: -0.00 (0.14), residues: 1384 sheet: -3.56 (0.43), residues: 64 loop : -2.48 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.023 0.001 TYR C 161 PHE 0.019 0.001 PHE C 504 TRP 0.028 0.001 TRP D 583 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00265 (20602) covalent geometry : angle 0.70613 (27945) hydrogen bonds : bond 0.03890 ( 780) hydrogen bonds : angle 4.54159 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 827 time to evaluate : 0.785 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 35 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 39 LEU cc_start: 0.9564 (tp) cc_final: 0.9195 (tp) REVERT: A 42 LYS cc_start: 0.9334 (tttt) cc_final: 0.8952 (pptt) REVERT: A 84 HIS cc_start: 0.8911 (m170) cc_final: 0.8639 (m170) REVERT: A 113 GLU cc_start: 0.9555 (tt0) cc_final: 0.9038 (tm-30) REVERT: A 150 THR cc_start: 0.9143 (t) cc_final: 0.8842 (t) REVERT: A 206 GLN cc_start: 0.9366 (mm-40) cc_final: 0.8761 (mm-40) REVERT: A 209 LYS cc_start: 0.8605 (mttt) cc_final: 0.8025 (ttmt) REVERT: A 215 MET cc_start: 0.9412 (mmm) cc_final: 0.8967 (mmm) REVERT: A 245 LYS cc_start: 0.8478 (mttt) cc_final: 0.7964 (mtpp) REVERT: A 259 LEU cc_start: 0.9574 (mm) cc_final: 0.9372 (mm) REVERT: A 260 MET cc_start: 0.9632 (tpt) cc_final: 0.9315 (mmm) REVERT: A 282 GLU cc_start: 0.8967 (mp0) cc_final: 0.8739 (mm-30) REVERT: A 300 LYS cc_start: 0.9143 (mttt) cc_final: 0.8645 (mppt) REVERT: A 301 LYS cc_start: 0.9353 (tptt) cc_final: 0.9012 (tmtt) REVERT: A 306 GLN cc_start: 0.8911 (pt0) cc_final: 0.8661 (mp10) REVERT: A 343 PHE cc_start: 0.9608 (t80) cc_final: 0.9295 (t80) REVERT: A 347 CYS cc_start: 0.8931 (m) cc_final: 0.8357 (m) REVERT: A 403 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8799 (tp30) REVERT: A 410 MET cc_start: 0.8970 (tpt) cc_final: 0.8214 (tpp) REVERT: A 435 MET cc_start: 0.8804 (mmt) cc_final: 0.8584 (mmp) REVERT: A 440 MET cc_start: 0.8623 (tpt) cc_final: 0.8237 (tpp) REVERT: A 454 MET cc_start: 0.9271 (mtt) cc_final: 0.8900 (mmt) REVERT: A 463 CYS cc_start: 0.9361 (m) cc_final: 0.9098 (m) REVERT: A 483 GLN cc_start: 0.9609 (tt0) cc_final: 0.9342 (tt0) REVERT: A 493 PHE cc_start: 0.9783 (t80) cc_final: 0.8889 (t80) REVERT: A 497 MET cc_start: 0.9387 (ttp) cc_final: 0.8868 (ttp) REVERT: A 515 GLU cc_start: 0.9172 (tp30) cc_final: 0.8624 (tp30) REVERT: A 518 GLU cc_start: 0.9365 (mp0) cc_final: 0.9143 (mp0) REVERT: A 526 TYR cc_start: 0.8638 (t80) cc_final: 0.8294 (t80) REVERT: A 537 PHE cc_start: 0.9572 (t80) cc_final: 0.8626 (t80) REVERT: A 541 ILE cc_start: 0.8782 (pt) cc_final: 0.8414 (mm) REVERT: A 605 GLU cc_start: 0.9345 (tt0) cc_final: 0.9067 (tt0) REVERT: A 631 LEU cc_start: 0.9443 (tt) cc_final: 0.9165 (tt) REVERT: B 57 ASP cc_start: 0.9090 (m-30) cc_final: 0.8639 (m-30) REVERT: B 70 CYS cc_start: 0.8335 (p) cc_final: 0.7916 (p) REVERT: B 113 GLU cc_start: 0.9492 (tt0) cc_final: 0.8999 (tm-30) REVERT: B 118 GLN cc_start: 0.9385 (tt0) cc_final: 0.9026 (tm-30) REVERT: B 123 ILE cc_start: 0.9540 (mt) cc_final: 0.9156 (mt) REVERT: B 128 GLN cc_start: 0.9098 (pt0) cc_final: 0.8185 (tm-30) REVERT: B 132 LEU cc_start: 0.9705 (tp) cc_final: 0.9352 (mt) REVERT: B 206 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9000 (mm110) REVERT: B 209 LYS cc_start: 0.9146 (mttt) cc_final: 0.8519 (ttmt) REVERT: B 245 LYS cc_start: 0.9165 (mttt) cc_final: 0.8592 (ptpp) REVERT: B 250 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 260 MET cc_start: 0.9579 (mmm) cc_final: 0.9109 (mmm) REVERT: B 294 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8649 (mt-10) REVERT: B 300 LYS cc_start: 0.8986 (mttt) cc_final: 0.8448 (mppt) REVERT: B 306 GLN cc_start: 0.8911 (pt0) cc_final: 0.8560 (mp10) REVERT: B 403 GLU cc_start: 0.9128 (tp30) cc_final: 0.8883 (tp30) REVERT: B 410 MET cc_start: 0.8866 (tmm) cc_final: 0.8531 (tmm) REVERT: B 440 MET cc_start: 0.9376 (tpp) cc_final: 0.9063 (tpp) REVERT: B 454 MET cc_start: 0.9386 (mmt) cc_final: 0.8657 (tpp) REVERT: B 463 CYS cc_start: 0.9343 (m) cc_final: 0.9124 (m) REVERT: B 483 GLN cc_start: 0.9604 (tt0) cc_final: 0.9194 (tp40) REVERT: B 497 MET cc_start: 0.9214 (ttp) cc_final: 0.8726 (ttp) REVERT: B 528 MET cc_start: 0.8162 (mmp) cc_final: 0.7262 (mmm) REVERT: B 537 PHE cc_start: 0.9425 (t80) cc_final: 0.8487 (t80) REVERT: B 541 ILE cc_start: 0.9028 (pt) cc_final: 0.8774 (pt) REVERT: C 34 ASP cc_start: 0.9402 (m-30) cc_final: 0.9201 (m-30) REVERT: C 35 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8892 (mp0) REVERT: C 42 LYS cc_start: 0.9269 (tttt) cc_final: 0.9013 (pttm) REVERT: C 93 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8776 (pm20) REVERT: C 96 MET cc_start: 0.9253 (mmt) cc_final: 0.8885 (tmm) REVERT: C 105 LEU cc_start: 0.9677 (tp) cc_final: 0.9463 (tp) REVERT: C 204 ILE cc_start: 0.9550 (mt) cc_final: 0.9292 (mt) REVERT: C 206 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8669 (mm-40) REVERT: C 209 LYS cc_start: 0.8761 (mttt) cc_final: 0.8102 (ttmt) REVERT: C 215 MET cc_start: 0.9353 (mmp) cc_final: 0.8938 (mmm) REVERT: C 246 LEU cc_start: 0.9692 (tp) cc_final: 0.9427 (tp) REVERT: C 250 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8529 (mm-30) REVERT: C 260 MET cc_start: 0.9668 (tpt) cc_final: 0.9331 (mmm) REVERT: C 300 LYS cc_start: 0.9037 (mttt) cc_final: 0.8569 (mppt) REVERT: C 301 LYS cc_start: 0.9316 (tptp) cc_final: 0.7966 (tmtt) REVERT: C 403 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8878 (tp30) REVERT: C 454 MET cc_start: 0.9394 (mmt) cc_final: 0.8909 (tpp) REVERT: C 463 CYS cc_start: 0.9227 (m) cc_final: 0.9007 (m) REVERT: C 483 GLN cc_start: 0.9619 (tt0) cc_final: 0.9374 (tt0) REVERT: C 497 MET cc_start: 0.9198 (ttp) cc_final: 0.8760 (ttp) REVERT: C 518 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8953 (tm-30) REVERT: C 537 PHE cc_start: 0.9498 (t80) cc_final: 0.8864 (t80) REVERT: C 538 LEU cc_start: 0.9000 (mp) cc_final: 0.8785 (mp) REVERT: C 541 ILE cc_start: 0.9107 (mm) cc_final: 0.8855 (mm) REVERT: C 570 MET cc_start: 0.9421 (mmp) cc_final: 0.9181 (mmm) REVERT: C 593 TRP cc_start: 0.9187 (t60) cc_final: 0.8846 (t60) REVERT: D 35 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8827 (mt-10) REVERT: D 93 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8840 (pm20) REVERT: D 96 MET cc_start: 0.9352 (mmp) cc_final: 0.8827 (mmm) REVERT: D 99 MET cc_start: 0.9086 (mtm) cc_final: 0.8685 (ptp) REVERT: D 113 GLU cc_start: 0.9576 (tt0) cc_final: 0.9269 (tm-30) REVERT: D 204 ILE cc_start: 0.9566 (mt) cc_final: 0.9337 (mt) REVERT: D 206 GLN cc_start: 0.9387 (mm-40) cc_final: 0.8729 (mm-40) REVERT: D 209 LYS cc_start: 0.8651 (mttt) cc_final: 0.8271 (mtpt) REVERT: D 215 MET cc_start: 0.9343 (mmp) cc_final: 0.8918 (mmm) REVERT: D 245 LYS cc_start: 0.8683 (mttt) cc_final: 0.8124 (ptpp) REVERT: D 246 LEU cc_start: 0.9692 (tp) cc_final: 0.9433 (tp) REVERT: D 250 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8337 (mm-30) REVERT: D 260 MET cc_start: 0.9665 (tpt) cc_final: 0.9336 (mmm) REVERT: D 300 LYS cc_start: 0.8999 (mttt) cc_final: 0.8481 (mppt) REVERT: D 301 LYS cc_start: 0.9206 (tptt) cc_final: 0.8609 (tptp) REVERT: D 367 LEU cc_start: 0.9346 (tp) cc_final: 0.9079 (tp) REVERT: D 403 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8764 (tp30) REVERT: D 410 MET cc_start: 0.9282 (tpt) cc_final: 0.8642 (tpp) REVERT: D 439 THR cc_start: 0.9739 (p) cc_final: 0.8584 (p) REVERT: D 442 MET cc_start: 0.9388 (ptm) cc_final: 0.8786 (ppp) REVERT: D 483 GLN cc_start: 0.9711 (tt0) cc_final: 0.9354 (tp40) REVERT: D 515 GLU cc_start: 0.9126 (tp30) cc_final: 0.8628 (tp30) REVERT: D 570 MET cc_start: 0.9440 (mmp) cc_final: 0.9126 (mmm) REVERT: D 583 TRP cc_start: 0.9132 (p-90) cc_final: 0.8693 (p-90) outliers start: 0 outliers final: 0 residues processed: 827 average time/residue: 0.1138 time to fit residues: 152.7643 Evaluate side-chains 681 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 464 ASN A 582 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 74 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.058665 restraints weight = 61320.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061610 restraints weight = 33801.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063920 restraints weight = 22320.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065501 restraints weight = 16288.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066872 restraints weight = 12805.703| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20602 Z= 0.122 Angle : 0.729 13.314 27945 Z= 0.354 Chirality : 0.045 0.192 3138 Planarity : 0.004 0.056 3522 Dihedral : 5.133 46.846 2928 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 are not related in a simple way. whole: -1.71 (0.17), residues: 2472 helix: -0.09 (0.14), residues: 1412 sheet: -3.50 (0.43), residues: 64 loop : -2.52 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 139 TYR 0.017 0.001 TYR B 324 PHE 0.018 0.001 PHE B 211 TRP 0.031 0.001 TRP B 583 HIS 0.010 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00262 (20602) covalent geometry : angle 0.72857 (27945) hydrogen bonds : bond 0.03766 ( 780) hydrogen bonds : angle 4.57623 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 806 time to evaluate : 0.745 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 39 LEU cc_start: 0.9559 (tp) cc_final: 0.9204 (tp) REVERT: A 42 LYS cc_start: 0.9373 (tttt) cc_final: 0.8992 (pptt) REVERT: A 84 HIS cc_start: 0.8901 (m170) cc_final: 0.8588 (m170) REVERT: A 99 MET cc_start: 0.8256 (ttt) cc_final: 0.7567 (tmm) REVERT: A 113 GLU cc_start: 0.9560 (tt0) cc_final: 0.9042 (tm-30) REVERT: A 150 THR cc_start: 0.9156 (t) cc_final: 0.8865 (t) REVERT: A 206 GLN cc_start: 0.9392 (mm-40) cc_final: 0.8818 (mm-40) REVERT: A 209 LYS cc_start: 0.8686 (mttt) cc_final: 0.8183 (ttmt) REVERT: A 215 MET cc_start: 0.9443 (mmm) cc_final: 0.9006 (mmm) REVERT: A 245 LYS cc_start: 0.8425 (mttt) cc_final: 0.8171 (mtpt) REVERT: A 260 MET cc_start: 0.9645 (tpt) cc_final: 0.9352 (mmm) REVERT: A 300 LYS cc_start: 0.9221 (mttt) cc_final: 0.8740 (mppt) REVERT: A 306 GLN cc_start: 0.8908 (pt0) cc_final: 0.8647 (mp10) REVERT: A 343 PHE cc_start: 0.9604 (t80) cc_final: 0.9281 (t80) REVERT: A 347 CYS cc_start: 0.8922 (m) cc_final: 0.8432 (m) REVERT: A 399 ILE cc_start: 0.9243 (mt) cc_final: 0.9012 (mt) REVERT: A 403 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8823 (tp30) REVERT: A 410 MET cc_start: 0.9093 (tpt) cc_final: 0.8323 (tpp) REVERT: A 435 MET cc_start: 0.8913 (mmt) cc_final: 0.8669 (mmp) REVERT: A 440 MET cc_start: 0.8679 (tpt) cc_final: 0.8330 (tpp) REVERT: A 454 MET cc_start: 0.9284 (mtt) cc_final: 0.8905 (mmm) REVERT: A 463 CYS cc_start: 0.9403 (m) cc_final: 0.9176 (m) REVERT: A 483 GLN cc_start: 0.9613 (tt0) cc_final: 0.9243 (mm-40) REVERT: A 493 PHE cc_start: 0.9691 (t80) cc_final: 0.8662 (t80) REVERT: A 497 MET cc_start: 0.9355 (ttp) cc_final: 0.8816 (ttp) REVERT: A 515 GLU cc_start: 0.9129 (tp30) cc_final: 0.8603 (tp30) REVERT: A 518 GLU cc_start: 0.9356 (mp0) cc_final: 0.9143 (mp0) REVERT: A 526 TYR cc_start: 0.8684 (t80) cc_final: 0.8372 (t80) REVERT: A 537 PHE cc_start: 0.9589 (t80) cc_final: 0.8667 (t80) REVERT: A 541 ILE cc_start: 0.8812 (pt) cc_final: 0.8475 (mm) REVERT: A 570 MET cc_start: 0.9577 (mmm) cc_final: 0.9132 (mmm) REVERT: A 605 GLU cc_start: 0.9364 (tt0) cc_final: 0.9098 (tt0) REVERT: B 57 ASP cc_start: 0.9075 (m-30) cc_final: 0.8600 (m-30) REVERT: B 70 CYS cc_start: 0.8542 (p) cc_final: 0.8155 (p) REVERT: B 113 GLU cc_start: 0.9497 (tt0) cc_final: 0.9028 (tm-30) REVERT: B 118 GLN cc_start: 0.9414 (tt0) cc_final: 0.9030 (tm-30) REVERT: B 123 ILE cc_start: 0.9527 (mt) cc_final: 0.9232 (mt) REVERT: B 128 GLN cc_start: 0.9026 (pt0) cc_final: 0.8095 (tm-30) REVERT: B 132 LEU cc_start: 0.9723 (tp) cc_final: 0.9440 (mt) REVERT: B 206 GLN cc_start: 0.9606 (mm-40) cc_final: 0.8799 (mm110) REVERT: B 209 LYS cc_start: 0.9120 (mttt) cc_final: 0.8530 (ttmt) REVERT: B 245 LYS cc_start: 0.9173 (mttt) cc_final: 0.8648 (ptpp) REVERT: B 250 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 260 MET cc_start: 0.9581 (mmm) cc_final: 0.9113 (mmm) REVERT: B 294 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8778 (mt-10) REVERT: B 300 LYS cc_start: 0.9046 (mttt) cc_final: 0.8501 (mppt) REVERT: B 301 LYS cc_start: 0.8896 (tptp) cc_final: 0.8626 (tmtt) REVERT: B 306 GLN cc_start: 0.8846 (pt0) cc_final: 0.8477 (mp10) REVERT: B 347 CYS cc_start: 0.8717 (p) cc_final: 0.8387 (p) REVERT: B 403 GLU cc_start: 0.9165 (tp30) cc_final: 0.8889 (tp30) REVERT: B 440 MET cc_start: 0.9392 (tpp) cc_final: 0.9088 (tpp) REVERT: B 454 MET cc_start: 0.9389 (mmt) cc_final: 0.8655 (tpp) REVERT: B 463 CYS cc_start: 0.9360 (m) cc_final: 0.9155 (m) REVERT: B 483 GLN cc_start: 0.9589 (tt0) cc_final: 0.9229 (tp40) REVERT: B 497 MET cc_start: 0.9150 (ttp) cc_final: 0.8660 (ttp) REVERT: B 528 MET cc_start: 0.8197 (mmp) cc_final: 0.7316 (mmm) REVERT: B 537 PHE cc_start: 0.9437 (t80) cc_final: 0.8461 (t80) REVERT: B 541 ILE cc_start: 0.9051 (pt) cc_final: 0.8802 (pt) REVERT: B 593 TRP cc_start: 0.9181 (t60) cc_final: 0.8561 (t60) REVERT: C 34 ASP cc_start: 0.9438 (m-30) cc_final: 0.9217 (m-30) REVERT: C 35 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8917 (mp0) REVERT: C 42 LYS cc_start: 0.9257 (tttt) cc_final: 0.9002 (pttm) REVERT: C 93 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8749 (pm20) REVERT: C 96 MET cc_start: 0.9262 (mmt) cc_final: 0.8909 (tmm) REVERT: C 204 ILE cc_start: 0.9543 (mt) cc_final: 0.9285 (mt) REVERT: C 206 GLN cc_start: 0.9316 (mm-40) cc_final: 0.8690 (mm-40) REVERT: C 209 LYS cc_start: 0.8774 (mttt) cc_final: 0.8087 (ttmt) REVERT: C 215 MET cc_start: 0.9357 (mmp) cc_final: 0.8946 (mmm) REVERT: C 246 LEU cc_start: 0.9700 (tp) cc_final: 0.9404 (tp) REVERT: C 250 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8514 (mm-30) REVERT: C 260 MET cc_start: 0.9670 (tpt) cc_final: 0.9332 (mmm) REVERT: C 300 LYS cc_start: 0.9021 (mttt) cc_final: 0.8553 (mppt) REVERT: C 301 LYS cc_start: 0.9157 (tptp) cc_final: 0.8547 (tptp) REVERT: C 403 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8918 (tp30) REVERT: C 410 MET cc_start: 0.9093 (tmm) cc_final: 0.8701 (ppp) REVERT: C 444 LEU cc_start: 0.9605 (mm) cc_final: 0.9386 (mm) REVERT: C 454 MET cc_start: 0.9426 (mmt) cc_final: 0.9017 (mmm) REVERT: C 463 CYS cc_start: 0.9274 (m) cc_final: 0.9043 (m) REVERT: C 483 GLN cc_start: 0.9620 (tt0) cc_final: 0.9386 (tt0) REVERT: C 497 MET cc_start: 0.9216 (ttp) cc_final: 0.8771 (ttp) REVERT: C 518 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8960 (tm-30) REVERT: C 537 PHE cc_start: 0.9507 (t80) cc_final: 0.8951 (t80) REVERT: C 570 MET cc_start: 0.9440 (mmp) cc_final: 0.9183 (mmm) REVERT: C 593 TRP cc_start: 0.9216 (t60) cc_final: 0.8904 (t60) REVERT: D 35 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8832 (mt-10) REVERT: D 93 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8781 (pm20) REVERT: D 96 MET cc_start: 0.9359 (mmp) cc_final: 0.8811 (mmm) REVERT: D 99 MET cc_start: 0.9069 (mtm) cc_final: 0.8696 (ptp) REVERT: D 113 GLU cc_start: 0.9585 (tt0) cc_final: 0.9294 (tm-30) REVERT: D 204 ILE cc_start: 0.9572 (mt) cc_final: 0.9330 (mt) REVERT: D 206 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8744 (mm-40) REVERT: D 209 LYS cc_start: 0.8649 (mttt) cc_final: 0.8212 (mtmt) REVERT: D 215 MET cc_start: 0.9371 (mmp) cc_final: 0.8989 (mmt) REVERT: D 245 LYS cc_start: 0.8634 (mttt) cc_final: 0.8083 (ptpp) REVERT: D 246 LEU cc_start: 0.9714 (tp) cc_final: 0.9410 (tp) REVERT: D 250 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8484 (mm-30) REVERT: D 259 LEU cc_start: 0.9624 (mm) cc_final: 0.9424 (mm) REVERT: D 260 MET cc_start: 0.9681 (tpt) cc_final: 0.9347 (mmm) REVERT: D 300 LYS cc_start: 0.9097 (mttt) cc_final: 0.8582 (mppt) REVERT: D 301 LYS cc_start: 0.9179 (tptt) cc_final: 0.8694 (tptp) REVERT: D 343 PHE cc_start: 0.9573 (t80) cc_final: 0.9355 (t80) REVERT: D 347 CYS cc_start: 0.8646 (m) cc_final: 0.8389 (m) REVERT: D 403 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8775 (tp30) REVERT: D 410 MET cc_start: 0.9251 (tpt) cc_final: 0.8713 (tpp) REVERT: D 442 MET cc_start: 0.9360 (ptm) cc_final: 0.9110 (ppp) REVERT: D 454 MET cc_start: 0.9391 (mmp) cc_final: 0.8963 (mmm) REVERT: D 483 GLN cc_start: 0.9707 (tt0) cc_final: 0.9347 (tp40) REVERT: D 485 MET cc_start: 0.9700 (mmm) cc_final: 0.9436 (mmt) REVERT: D 497 MET cc_start: 0.8673 (tmm) cc_final: 0.8109 (tmm) REVERT: D 515 GLU cc_start: 0.9112 (tp30) cc_final: 0.8631 (tp30) REVERT: D 536 LEU cc_start: 0.9731 (mt) cc_final: 0.9526 (mt) REVERT: D 570 MET cc_start: 0.9474 (mmp) cc_final: 0.9136 (mmm) REVERT: D 583 TRP cc_start: 0.9145 (p-90) cc_final: 0.8661 (p-90) REVERT: D 631 LEU cc_start: 0.9455 (tt) cc_final: 0.9097 (tt) outliers start: 0 outliers final: 0 residues processed: 806 average time/residue: 0.1150 time to fit residues: 150.3057 Evaluate side-chains 679 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 9 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 582 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 582 HIS D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058959 restraints weight = 61014.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.061917 restraints weight = 33717.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064205 restraints weight = 22282.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065989 restraints weight = 16367.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067254 restraints weight = 12719.223| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20602 Z= 0.125 Angle : 0.732 13.714 27945 Z= 0.357 Chirality : 0.045 0.190 3138 Planarity : 0.004 0.057 3522 Dihedral : 5.025 41.376 2928 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 are not related in a simple way. whole: -1.57 (0.17), residues: 2472 helix: 0.01 (0.14), residues: 1396 sheet: -3.94 (0.54), residues: 48 loop : -2.41 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 606 TYR 0.023 0.001 TYR B 324 PHE 0.018 0.001 PHE B 630 TRP 0.023 0.001 TRP B 583 HIS 0.008 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00269 (20602) covalent geometry : angle 0.73208 (27945) hydrogen bonds : bond 0.03693 ( 780) hydrogen bonds : angle 4.53840 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 809 time to evaluate : 0.743 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 49 LEU cc_start: 0.9424 (pt) cc_final: 0.9027 (tp) REVERT: A 50 LEU cc_start: 0.9578 (mp) cc_final: 0.9346 (mp) REVERT: A 84 HIS cc_start: 0.8937 (m170) cc_final: 0.8647 (m170) REVERT: A 99 MET cc_start: 0.8263 (ttt) cc_final: 0.7662 (tmm) REVERT: A 113 GLU cc_start: 0.9570 (tt0) cc_final: 0.9055 (tm-30) REVERT: A 150 THR cc_start: 0.9145 (t) cc_final: 0.8849 (t) REVERT: A 206 GLN cc_start: 0.9375 (mm-40) cc_final: 0.8795 (mm-40) REVERT: A 209 LYS cc_start: 0.8702 (mttt) cc_final: 0.8317 (ttmt) REVERT: A 215 MET cc_start: 0.9448 (mmm) cc_final: 0.9028 (mmm) REVERT: A 245 LYS cc_start: 0.8665 (mttt) cc_final: 0.8460 (mtpt) REVERT: A 259 LEU cc_start: 0.9608 (mm) cc_final: 0.9403 (mm) REVERT: A 260 MET cc_start: 0.9653 (tpt) cc_final: 0.9346 (mmm) REVERT: A 300 LYS cc_start: 0.9221 (mttt) cc_final: 0.8741 (mppt) REVERT: A 399 ILE cc_start: 0.9273 (mt) cc_final: 0.9051 (mt) REVERT: A 403 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8815 (tp30) REVERT: A 410 MET cc_start: 0.8972 (tpt) cc_final: 0.8383 (tpp) REVERT: A 454 MET cc_start: 0.9305 (mtt) cc_final: 0.8941 (mmm) REVERT: A 463 CYS cc_start: 0.9438 (m) cc_final: 0.9183 (m) REVERT: A 483 GLN cc_start: 0.9600 (tt0) cc_final: 0.9226 (mm-40) REVERT: A 493 PHE cc_start: 0.9721 (t80) cc_final: 0.8883 (t80) REVERT: A 497 MET cc_start: 0.9362 (ttp) cc_final: 0.8863 (ttp) REVERT: A 515 GLU cc_start: 0.9112 (tp30) cc_final: 0.8557 (tp30) REVERT: A 518 GLU cc_start: 0.9372 (mp0) cc_final: 0.9171 (mp0) REVERT: A 526 TYR cc_start: 0.8640 (t80) cc_final: 0.8347 (t80) REVERT: A 537 PHE cc_start: 0.9568 (t80) cc_final: 0.8655 (t80) REVERT: A 541 ILE cc_start: 0.8836 (pt) cc_final: 0.8446 (mm) REVERT: A 605 GLU cc_start: 0.9346 (tt0) cc_final: 0.9063 (tt0) REVERT: B 57 ASP cc_start: 0.9072 (m-30) cc_final: 0.8574 (m-30) REVERT: B 70 CYS cc_start: 0.8515 (p) cc_final: 0.8161 (p) REVERT: B 113 GLU cc_start: 0.9489 (tt0) cc_final: 0.8983 (tm-30) REVERT: B 118 GLN cc_start: 0.9438 (tt0) cc_final: 0.9002 (tm-30) REVERT: B 123 ILE cc_start: 0.9506 (mt) cc_final: 0.9226 (mt) REVERT: B 128 GLN cc_start: 0.8964 (pt0) cc_final: 0.7976 (tm-30) REVERT: B 206 GLN cc_start: 0.9556 (mm-40) cc_final: 0.8738 (mm110) REVERT: B 209 LYS cc_start: 0.9115 (mttt) cc_final: 0.8740 (mtpt) REVERT: B 245 LYS cc_start: 0.9157 (mttt) cc_final: 0.8608 (ptpp) REVERT: B 250 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 260 MET cc_start: 0.9580 (mmm) cc_final: 0.9132 (mmm) REVERT: B 294 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8770 (mt-10) REVERT: B 300 LYS cc_start: 0.9084 (mttt) cc_final: 0.8556 (mppt) REVERT: B 306 GLN cc_start: 0.8871 (pt0) cc_final: 0.8584 (mp10) REVERT: B 403 GLU cc_start: 0.9182 (tp30) cc_final: 0.8904 (tp30) REVERT: B 440 MET cc_start: 0.9400 (tpp) cc_final: 0.9119 (tpp) REVERT: B 454 MET cc_start: 0.9372 (mmt) cc_final: 0.8678 (tpp) REVERT: B 463 CYS cc_start: 0.9372 (m) cc_final: 0.9123 (m) REVERT: B 483 GLN cc_start: 0.9629 (tt0) cc_final: 0.9311 (tp-100) REVERT: B 497 MET cc_start: 0.9123 (ttp) cc_final: 0.8644 (ttp) REVERT: B 528 MET cc_start: 0.8193 (mmp) cc_final: 0.7315 (mmm) REVERT: B 537 PHE cc_start: 0.9428 (t80) cc_final: 0.8362 (t80) REVERT: B 541 ILE cc_start: 0.8848 (pt) cc_final: 0.8540 (pt) REVERT: B 580 ASP cc_start: 0.9046 (t0) cc_final: 0.8449 (t0) REVERT: B 583 TRP cc_start: 0.8949 (p-90) cc_final: 0.8706 (p-90) REVERT: B 593 TRP cc_start: 0.9181 (t60) cc_final: 0.8575 (t60) REVERT: C 35 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8958 (mt-10) REVERT: C 93 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8732 (pm20) REVERT: C 96 MET cc_start: 0.9248 (mmt) cc_final: 0.8892 (tmm) REVERT: C 204 ILE cc_start: 0.9532 (mt) cc_final: 0.9281 (mt) REVERT: C 206 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8667 (mm-40) REVERT: C 209 LYS cc_start: 0.8796 (mttt) cc_final: 0.8162 (ttmt) REVERT: C 215 MET cc_start: 0.9353 (mmp) cc_final: 0.8943 (mmt) REVERT: C 246 LEU cc_start: 0.9692 (tp) cc_final: 0.9361 (tp) REVERT: C 250 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 259 LEU cc_start: 0.9575 (mm) cc_final: 0.9319 (mm) REVERT: C 260 MET cc_start: 0.9659 (tpt) cc_final: 0.9320 (mmm) REVERT: C 300 LYS cc_start: 0.8936 (mttt) cc_final: 0.8480 (mppt) REVERT: C 301 LYS cc_start: 0.9034 (tptp) cc_final: 0.8641 (tmtt) REVERT: C 303 GLU cc_start: 0.9296 (pm20) cc_final: 0.8833 (pm20) REVERT: C 323 ARG cc_start: 0.9004 (ttm170) cc_final: 0.8378 (ptm160) REVERT: C 403 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8930 (tp30) REVERT: C 410 MET cc_start: 0.8971 (tmm) cc_final: 0.8746 (ppp) REVERT: C 444 LEU cc_start: 0.9596 (mm) cc_final: 0.9353 (mm) REVERT: C 454 MET cc_start: 0.9385 (mmt) cc_final: 0.8955 (mmm) REVERT: C 463 CYS cc_start: 0.9257 (m) cc_final: 0.9018 (m) REVERT: C 483 GLN cc_start: 0.9597 (tt0) cc_final: 0.9374 (tt0) REVERT: C 497 MET cc_start: 0.9208 (ttp) cc_final: 0.8739 (ttp) REVERT: C 518 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8977 (tm-30) REVERT: C 537 PHE cc_start: 0.9508 (t80) cc_final: 0.8920 (t80) REVERT: C 570 MET cc_start: 0.9445 (mmp) cc_final: 0.9168 (mmm) REVERT: C 593 TRP cc_start: 0.9232 (t60) cc_final: 0.8929 (t60) REVERT: D 34 ASP cc_start: 0.9459 (m-30) cc_final: 0.9160 (m-30) REVERT: D 35 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8812 (mt-10) REVERT: D 96 MET cc_start: 0.9354 (mmp) cc_final: 0.8817 (mmm) REVERT: D 99 MET cc_start: 0.9060 (mtm) cc_final: 0.8728 (ptp) REVERT: D 113 GLU cc_start: 0.9587 (tt0) cc_final: 0.9282 (tm-30) REVERT: D 204 ILE cc_start: 0.9550 (mt) cc_final: 0.9310 (mt) REVERT: D 206 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8697 (mm-40) REVERT: D 209 LYS cc_start: 0.8700 (mttt) cc_final: 0.8325 (mtpt) REVERT: D 215 MET cc_start: 0.9382 (mmp) cc_final: 0.8994 (mmt) REVERT: D 246 LEU cc_start: 0.9709 (tp) cc_final: 0.9377 (tp) REVERT: D 250 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8632 (mm-30) REVERT: D 259 LEU cc_start: 0.9630 (mm) cc_final: 0.9358 (mm) REVERT: D 260 MET cc_start: 0.9673 (tpt) cc_final: 0.9342 (mmm) REVERT: D 300 LYS cc_start: 0.9143 (mttt) cc_final: 0.8638 (mppt) REVERT: D 301 LYS cc_start: 0.9071 (tptt) cc_final: 0.8672 (ttpt) REVERT: D 323 ARG cc_start: 0.9064 (ttm170) cc_final: 0.8666 (ttm110) REVERT: D 343 PHE cc_start: 0.9563 (t80) cc_final: 0.9340 (t80) REVERT: D 347 CYS cc_start: 0.8605 (m) cc_final: 0.8348 (m) REVERT: D 403 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8774 (tp30) REVERT: D 410 MET cc_start: 0.9271 (tpt) cc_final: 0.8711 (tpp) REVERT: D 421 LEU cc_start: 0.9222 (tp) cc_final: 0.9005 (tp) REVERT: D 442 MET cc_start: 0.9349 (ptm) cc_final: 0.9137 (ppp) REVERT: D 454 MET cc_start: 0.9401 (mmp) cc_final: 0.9008 (mmm) REVERT: D 483 GLN cc_start: 0.9685 (tt0) cc_final: 0.9313 (tp40) REVERT: D 497 MET cc_start: 0.8653 (tmm) cc_final: 0.8093 (tmm) REVERT: D 515 GLU cc_start: 0.9175 (tp30) cc_final: 0.8736 (tp30) REVERT: D 570 MET cc_start: 0.9475 (mmp) cc_final: 0.9138 (mmm) REVERT: D 583 TRP cc_start: 0.9175 (p-90) cc_final: 0.8628 (p-90) REVERT: D 588 GLU cc_start: 0.9489 (pp20) cc_final: 0.9148 (pp20) outliers start: 0 outliers final: 0 residues processed: 809 average time/residue: 0.1116 time to fit residues: 146.9646 Evaluate side-chains 677 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 242 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 582 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 572 ASN D 74 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055981 restraints weight = 65294.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.058758 restraints weight = 36409.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060836 restraints weight = 24401.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.062295 restraints weight = 18064.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.063651 restraints weight = 14396.899| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20602 Z= 0.176 Angle : 0.757 10.922 27945 Z= 0.379 Chirality : 0.046 0.220 3138 Planarity : 0.004 0.052 3522 Dihedral : 5.158 37.208 2928 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.54 % 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 are not related in a simple way. whole: -1.75 (0.17), residues: 2472 helix: -0.13 (0.14), residues: 1428 sheet: -3.44 (0.37), residues: 84 loop : -2.51 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 606 TYR 0.018 0.001 TYR D 526 PHE 0.021 0.001 PHE B 162 TRP 0.026 0.001 TRP B 583 HIS 0.012 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00367 (20602) covalent geometry : angle 0.75715 (27945) hydrogen bonds : bond 0.03608 ( 780) hydrogen bonds : angle 4.75813 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 779 time to evaluate : 0.540 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 39 LEU cc_start: 0.9612 (tp) cc_final: 0.9244 (tp) REVERT: A 42 LYS cc_start: 0.9344 (tttt) cc_final: 0.8993 (pttt) REVERT: A 84 HIS cc_start: 0.8876 (m170) cc_final: 0.8557 (m170) REVERT: A 93 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8586 (pm20) REVERT: A 99 MET cc_start: 0.8396 (ttt) cc_final: 0.7559 (tmm) REVERT: A 113 GLU cc_start: 0.9581 (tt0) cc_final: 0.9057 (tm-30) REVERT: A 150 THR cc_start: 0.9222 (t) cc_final: 0.8932 (t) REVERT: A 206 GLN cc_start: 0.9389 (mm-40) cc_final: 0.8953 (mm-40) REVERT: A 209 LYS cc_start: 0.8789 (mttt) cc_final: 0.8305 (ttmt) REVERT: A 215 MET cc_start: 0.9442 (mmm) cc_final: 0.9025 (mmm) REVERT: A 259 LEU cc_start: 0.9641 (mm) cc_final: 0.9386 (mm) REVERT: A 260 MET cc_start: 0.9662 (tpt) cc_final: 0.9387 (mmm) REVERT: A 300 LYS cc_start: 0.9221 (mttt) cc_final: 0.8720 (mppt) REVERT: A 323 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.8229 (ptm160) REVERT: A 343 PHE cc_start: 0.9646 (t80) cc_final: 0.9419 (t80) REVERT: A 403 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8883 (tp30) REVERT: A 410 MET cc_start: 0.9092 (tpt) cc_final: 0.8428 (tpp) REVERT: A 440 MET cc_start: 0.9188 (tpp) cc_final: 0.8845 (tpp) REVERT: A 454 MET cc_start: 0.9365 (mtt) cc_final: 0.9013 (mmt) REVERT: A 463 CYS cc_start: 0.9445 (m) cc_final: 0.9211 (m) REVERT: A 483 GLN cc_start: 0.9619 (tt0) cc_final: 0.9319 (tt0) REVERT: A 493 PHE cc_start: 0.9722 (t80) cc_final: 0.8687 (t80) REVERT: A 497 MET cc_start: 0.9388 (ttp) cc_final: 0.8782 (ttp) REVERT: A 515 GLU cc_start: 0.9157 (tp30) cc_final: 0.8491 (tp30) REVERT: A 518 GLU cc_start: 0.9385 (mp0) cc_final: 0.9148 (mp0) REVERT: A 526 TYR cc_start: 0.8714 (t80) cc_final: 0.8416 (t80) REVERT: A 537 PHE cc_start: 0.9582 (t80) cc_final: 0.8649 (t80) REVERT: A 605 GLU cc_start: 0.9371 (tt0) cc_final: 0.9146 (tt0) REVERT: B 57 ASP cc_start: 0.9115 (m-30) cc_final: 0.8620 (m-30) REVERT: B 70 CYS cc_start: 0.8532 (p) cc_final: 0.8122 (p) REVERT: B 113 GLU cc_start: 0.9504 (tt0) cc_final: 0.9138 (tm-30) REVERT: B 118 GLN cc_start: 0.9503 (tt0) cc_final: 0.9097 (tm-30) REVERT: B 123 ILE cc_start: 0.9541 (mt) cc_final: 0.9294 (mt) REVERT: B 206 GLN cc_start: 0.9574 (mm-40) cc_final: 0.8758 (mm110) REVERT: B 209 LYS cc_start: 0.9130 (mttt) cc_final: 0.8714 (mtmt) REVERT: B 245 LYS cc_start: 0.9182 (mttt) cc_final: 0.8622 (ptpp) REVERT: B 246 LEU cc_start: 0.9741 (tp) cc_final: 0.9466 (tp) REVERT: B 250 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 260 MET cc_start: 0.9590 (mmm) cc_final: 0.9118 (mmm) REVERT: B 290 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8976 (mm-40) REVERT: B 294 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8675 (tt0) REVERT: B 300 LYS cc_start: 0.9088 (mttt) cc_final: 0.8587 (mppt) REVERT: B 306 GLN cc_start: 0.8968 (pt0) cc_final: 0.8698 (mp10) REVERT: B 347 CYS cc_start: 0.8817 (p) cc_final: 0.8564 (p) REVERT: B 403 GLU cc_start: 0.9164 (tp30) cc_final: 0.8878 (tp30) REVERT: B 440 MET cc_start: 0.9394 (tpp) cc_final: 0.9119 (tpp) REVERT: B 454 MET cc_start: 0.9409 (mmt) cc_final: 0.8742 (tpp) REVERT: B 463 CYS cc_start: 0.9394 (m) cc_final: 0.9116 (m) REVERT: B 483 GLN cc_start: 0.9637 (tt0) cc_final: 0.9370 (tp-100) REVERT: B 497 MET cc_start: 0.9193 (ttp) cc_final: 0.8719 (ttp) REVERT: B 528 MET cc_start: 0.8264 (mmp) cc_final: 0.7375 (mmm) REVERT: B 537 PHE cc_start: 0.9411 (t80) cc_final: 0.8392 (t80) REVERT: B 541 ILE cc_start: 0.8879 (pt) cc_final: 0.8615 (pt) REVERT: B 593 TRP cc_start: 0.9212 (t60) cc_final: 0.8611 (t60) REVERT: C 35 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8994 (mt-10) REVERT: C 93 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8772 (pm20) REVERT: C 96 MET cc_start: 0.9326 (mmt) cc_final: 0.9021 (tmm) REVERT: C 204 ILE cc_start: 0.9566 (mt) cc_final: 0.9339 (mt) REVERT: C 206 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8541 (mm-40) REVERT: C 209 LYS cc_start: 0.8904 (mttt) cc_final: 0.8385 (ttmt) REVERT: C 215 MET cc_start: 0.9297 (mmp) cc_final: 0.8850 (mmm) REVERT: C 246 LEU cc_start: 0.9710 (tp) cc_final: 0.9376 (tp) REVERT: C 259 LEU cc_start: 0.9642 (mm) cc_final: 0.9334 (mm) REVERT: C 260 MET cc_start: 0.9654 (tpt) cc_final: 0.9333 (mmm) REVERT: C 300 LYS cc_start: 0.9016 (mttt) cc_final: 0.8561 (mppt) REVERT: C 303 GLU cc_start: 0.9329 (pm20) cc_final: 0.8720 (pp20) REVERT: C 403 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8947 (tp30) REVERT: C 444 LEU cc_start: 0.9603 (mm) cc_final: 0.9370 (mm) REVERT: C 454 MET cc_start: 0.9390 (mmt) cc_final: 0.9011 (mmm) REVERT: C 463 CYS cc_start: 0.9300 (m) cc_final: 0.9066 (m) REVERT: C 483 GLN cc_start: 0.9609 (tt0) cc_final: 0.9335 (tp40) REVERT: C 497 MET cc_start: 0.9220 (ttp) cc_final: 0.8765 (ttp) REVERT: C 518 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8989 (tm-30) REVERT: C 537 PHE cc_start: 0.9546 (t80) cc_final: 0.8906 (t80) REVERT: C 570 MET cc_start: 0.9554 (mmp) cc_final: 0.9176 (mmm) REVERT: C 578 MET cc_start: 0.9624 (mtm) cc_final: 0.9050 (mtm) REVERT: C 593 TRP cc_start: 0.9238 (t60) cc_final: 0.9029 (t60) REVERT: C 605 GLU cc_start: 0.9284 (tt0) cc_final: 0.9082 (tt0) REVERT: C 631 LEU cc_start: 0.9525 (tt) cc_final: 0.9265 (tt) REVERT: D 35 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8878 (mt-10) REVERT: D 70 CYS cc_start: 0.8739 (t) cc_final: 0.8534 (t) REVERT: D 96 MET cc_start: 0.9419 (mmp) cc_final: 0.8923 (mmm) REVERT: D 113 GLU cc_start: 0.9581 (tt0) cc_final: 0.9278 (tm-30) REVERT: D 204 ILE cc_start: 0.9595 (mt) cc_final: 0.9382 (mt) REVERT: D 206 GLN cc_start: 0.9375 (mm-40) cc_final: 0.8765 (mm-40) REVERT: D 209 LYS cc_start: 0.8770 (mttt) cc_final: 0.8427 (mtmt) REVERT: D 215 MET cc_start: 0.9363 (mmp) cc_final: 0.8938 (mmm) REVERT: D 245 LYS cc_start: 0.8734 (mttt) cc_final: 0.8320 (ptpp) REVERT: D 246 LEU cc_start: 0.9728 (tp) cc_final: 0.9450 (tp) REVERT: D 250 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 259 LEU cc_start: 0.9636 (mm) cc_final: 0.9379 (mm) REVERT: D 260 MET cc_start: 0.9691 (tpt) cc_final: 0.9378 (mmm) REVERT: D 300 LYS cc_start: 0.9253 (mttt) cc_final: 0.8736 (mppt) REVERT: D 301 LYS cc_start: 0.9107 (tptt) cc_final: 0.8881 (ttpt) REVERT: D 323 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8853 (ttm170) REVERT: D 343 PHE cc_start: 0.9591 (t80) cc_final: 0.9352 (t80) REVERT: D 347 CYS cc_start: 0.8647 (m) cc_final: 0.8358 (m) REVERT: D 367 LEU cc_start: 0.9380 (tp) cc_final: 0.9104 (tp) REVERT: D 403 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8821 (tp30) REVERT: D 410 MET cc_start: 0.9266 (tpt) cc_final: 0.8725 (tpp) REVERT: D 439 THR cc_start: 0.9773 (p) cc_final: 0.9297 (p) REVERT: D 442 MET cc_start: 0.9394 (ptm) cc_final: 0.8835 (ppp) REVERT: D 454 MET cc_start: 0.9466 (mmp) cc_final: 0.9046 (mmm) REVERT: D 483 GLN cc_start: 0.9692 (tt0) cc_final: 0.9342 (tp40) REVERT: D 485 MET cc_start: 0.9539 (mmm) cc_final: 0.9289 (mmt) REVERT: D 497 MET cc_start: 0.8674 (tmm) cc_final: 0.8158 (tmm) REVERT: D 515 GLU cc_start: 0.9141 (tp30) cc_final: 0.8613 (tp30) REVERT: D 570 MET cc_start: 0.9553 (mmp) cc_final: 0.9151 (mmm) REVERT: D 588 GLU cc_start: 0.9541 (pp20) cc_final: 0.9179 (pp20) REVERT: D 631 LEU cc_start: 0.9403 (tt) cc_final: 0.9173 (tt) outliers start: 1 outliers final: 0 residues processed: 780 average time/residue: 0.1153 time to fit residues: 146.2207 Evaluate side-chains 664 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 175 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057723 restraints weight = 62223.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.060624 restraints weight = 34516.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.062814 restraints weight = 22974.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.064448 restraints weight = 16859.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065790 restraints weight = 13213.833| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20602 Z= 0.126 Angle : 0.751 11.175 27945 Z= 0.364 Chirality : 0.045 0.214 3138 Planarity : 0.004 0.053 3522 Dihedral : 4.966 33.851 2928 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 are not related in a simple way. whole: -1.63 (0.17), residues: 2472 helix: -0.00 (0.14), residues: 1424 sheet: -3.36 (0.37), residues: 84 loop : -2.51 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 606 TYR 0.022 0.001 TYR B 324 PHE 0.026 0.001 PHE A 508 TRP 0.035 0.001 TRP D 583 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00271 (20602) covalent geometry : angle 0.75118 (27945) hydrogen bonds : bond 0.03675 ( 780) hydrogen bonds : angle 4.56512 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.10 seconds wall clock time: 62 minutes 58.13 seconds (3778.13 seconds total)