Starting phenix.real_space_refine on Sat Sep 28 19:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_22666_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_22666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_22666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_22666_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/09_2024/7k4e_22666_neut.cif" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.73, per 1000 atoms: 0.58 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: 4.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.89 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: 5.21 Time building geometry restraints manager: 5.27 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 638 or resid 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: 0.830 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.890 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- 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= 0.543 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 : 5.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (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 TRP 0.022 0.002 TRP C 629 HIS 0.007 0.002 HIS D 522 PHE 0.015 0.002 PHE A 523 TYR 0.014 0.002 TYR D 623 ARG 0.004 0.001 ARG B 385 *********************** 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 fitting. rotamer outliers: 12 poor density : 1064 time to evaluate : 2.035 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: 0.8541 (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: 0.9692 (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: 0.9541 (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: 0.8272 (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: 0.8473 (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: 0.2904 time to fit residues: 474.8672 Evaluate side-chains 740 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 732 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 572 ASN A 582 HIS A 596 GLN B 74 GLN B 91 ASN B 118 GLN B 201 HIS ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 265 HIS C 572 ASN C 582 HIS ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN D 74 GLN D 118 GLN D 127 ASN D 201 HIS D 217 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20602 Z= 0.238 Angle : 0.765 8.030 27945 Z= 0.398 Chirality : 0.046 0.207 3138 Planarity : 0.006 0.068 3522 Dihedral : 7.714 109.131 2928 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.15), residues: 2472 helix: -1.41 (0.13), residues: 1344 sheet: -4.12 (0.55), residues: 48 loop : -2.80 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.012 0.001 HIS B 522 PHE 0.021 0.002 PHE C 211 TYR 0.015 0.001 TYR C 526 ARG 0.010 0.001 ARG D 470 *********************** 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 924 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 922 time to evaluate : 2.142 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: symmetry clash REVERT: A 93 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9143 (pm20) REVERT: A 113 GLU cc_start: 0.9327 (tt0) cc_final: 0.8884 (tm-30) REVERT: A 122 HIS cc_start: 0.9560 (m170) cc_final: 0.9275 (m170) REVERT: A 146 ARG cc_start: 0.9387 (mtt180) cc_final: 0.8891 (mmm-85) REVERT: A 169 PHE cc_start: 0.9431 (m-80) cc_final: 0.8663 (m-80) REVERT: A 215 MET cc_start: 0.9431 (mmm) cc_final: 0.8958 (mmm) REVERT: A 245 LYS cc_start: 0.8533 (mttt) cc_final: 0.7957 (mtpp) REVERT: A 263 ARG cc_start: 0.9330 (mmt180) cc_final: 0.9108 (mmp80) REVERT: A 300 LYS cc_start: 0.9011 (mttt) cc_final: 0.8564 (mppt) REVERT: A 303 GLU cc_start: 0.9433 (tt0) cc_final: 0.9224 (tp30) REVERT: A 306 GLN cc_start: 0.9012 (pt0) cc_final: 0.8494 (mp10) REVERT: A 336 TYR cc_start: 0.9197 (t80) cc_final: 0.8926 (t80) REVERT: A 382 ASP cc_start: 0.7605 (m-30) cc_final: 0.7067 (m-30) REVERT: A 403 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8892 (tp30) REVERT: A 421 LEU cc_start: 0.9123 (tt) cc_final: 0.8793 (pp) REVERT: A 437 LEU cc_start: 0.9656 (mm) cc_final: 0.9372 (mp) REVERT: A 440 MET cc_start: 0.9053 (ppp) cc_final: 0.8832 (tpt) REVERT: A 454 MET cc_start: 0.9291 (mtt) cc_final: 0.8880 (mmt) REVERT: A 458 LEU cc_start: 0.9843 (mm) cc_final: 0.9636 (mm) REVERT: A 463 CYS cc_start: 0.9313 (m) cc_final: 0.9100 (m) REVERT: A 465 VAL cc_start: 0.9612 (t) cc_final: 0.9386 (t) REVERT: A 466 MET cc_start: 0.9722 (mtt) cc_final: 0.9383 (mmm) REVERT: A 483 GLN cc_start: 0.9705 (tt0) cc_final: 0.9386 (tt0) REVERT: A 494 CYS cc_start: 0.9223 (t) cc_final: 0.8944 (p) REVERT: A 497 MET cc_start: 0.9419 (ttp) cc_final: 0.8743 (ttp) REVERT: A 537 PHE cc_start: 0.9578 (t80) cc_final: 0.8449 (t80) REVERT: A 551 LEU cc_start: 0.8044 (mt) cc_final: 0.7729 (mp) REVERT: A 569 LEU cc_start: 0.9815 (tp) cc_final: 0.9605 (tp) REVERT: A 577 MET cc_start: 0.9176 (mmm) cc_final: 0.8962 (mmt) REVERT: A 580 ASP cc_start: 0.8712 (m-30) cc_final: 0.8274 (m-30) REVERT: A 605 GLU cc_start: 0.9268 (tt0) cc_final: 0.9024 (mt-10) REVERT: B 57 ASP cc_start: 0.8976 (m-30) cc_final: 0.8706 (m-30) REVERT: B 93 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8970 (pm20) REVERT: B 96 MET cc_start: 0.9622 (mmt) cc_final: 0.9348 (mmm) REVERT: B 99 MET cc_start: 0.9371 (mtm) cc_final: 0.8790 (tpp) REVERT: B 113 GLU cc_start: 0.9514 (tt0) cc_final: 0.9142 (tm-30) REVERT: B 118 GLN cc_start: 0.9356 (tt0) cc_final: 0.8840 (tp40) REVERT: B 123 ILE cc_start: 0.9555 (mt) cc_final: 0.9202 (mt) REVERT: B 128 GLN cc_start: 0.9151 (pt0) cc_final: 0.8445 (tm-30) REVERT: B 167 LEU cc_start: 0.9662 (pt) cc_final: 0.9441 (tt) REVERT: B 174 ASN cc_start: 0.8848 (t0) cc_final: 0.8278 (t0) REVERT: B 175 SER cc_start: 0.8701 (p) cc_final: 0.8436 (t) REVERT: B 182 LEU cc_start: 0.9726 (mm) cc_final: 0.9446 (mm) REVERT: B 204 ILE cc_start: 0.9567 (mt) cc_final: 0.9305 (mt) REVERT: B 209 LYS cc_start: 0.9332 (mttt) cc_final: 0.8799 (ttmt) REVERT: B 219 LEU cc_start: 0.9769 (mt) cc_final: 0.9477 (mm) REVERT: B 245 LYS cc_start: 0.9171 (mttt) cc_final: 0.8773 (ptpp) REVERT: B 246 LEU cc_start: 0.9648 (tp) cc_final: 0.9378 (tp) REVERT: B 255 MET cc_start: 0.9061 (tpt) cc_final: 0.8839 (tpp) REVERT: B 259 LEU cc_start: 0.9714 (mm) cc_final: 0.9376 (mm) REVERT: B 260 MET cc_start: 0.9601 (mmm) cc_final: 0.9109 (mmm) REVERT: B 294 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 297 ILE cc_start: 0.9520 (pt) cc_final: 0.9223 (tp) REVERT: B 300 LYS cc_start: 0.8950 (mttt) cc_final: 0.8535 (mppt) REVERT: B 306 GLN cc_start: 0.8930 (pt0) cc_final: 0.8461 (mp10) REVERT: B 372 LEU cc_start: 0.9385 (pp) cc_final: 0.8895 (tt) REVERT: B 403 GLU cc_start: 0.8890 (tp30) cc_final: 0.8648 (tp30) REVERT: B 410 MET cc_start: 0.8999 (tmm) cc_final: 0.8214 (tmm) REVERT: B 421 LEU cc_start: 0.9236 (tt) cc_final: 0.8817 (tt) REVERT: B 454 MET cc_start: 0.9562 (mmt) cc_final: 0.8927 (tpp) REVERT: B 463 CYS cc_start: 0.9341 (m) cc_final: 0.9128 (m) REVERT: B 483 GLN cc_start: 0.9717 (tt0) cc_final: 0.9439 (mm-40) REVERT: B 494 CYS cc_start: 0.8991 (t) cc_final: 0.8741 (p) REVERT: B 497 MET cc_start: 0.9267 (ttp) cc_final: 0.8735 (ttp) REVERT: B 526 TYR cc_start: 0.9017 (t80) cc_final: 0.8773 (t80) REVERT: B 528 MET cc_start: 0.8415 (mmp) cc_final: 0.8093 (tpp) REVERT: B 537 PHE cc_start: 0.9392 (t80) cc_final: 0.8310 (t80) REVERT: B 538 LEU cc_start: 0.9290 (mp) cc_final: 0.8830 (mp) REVERT: B 554 MET cc_start: 0.8823 (tpt) cc_final: 0.8508 (tpt) REVERT: B 568 LEU cc_start: 0.9562 (tp) cc_final: 0.9360 (tp) REVERT: B 570 MET cc_start: 0.9254 (mmp) cc_final: 0.9004 (mmm) REVERT: B 574 LEU cc_start: 0.9884 (tp) cc_final: 0.9671 (tp) REVERT: C 35 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8948 (mp0) REVERT: C 84 HIS cc_start: 0.9170 (m90) cc_final: 0.8831 (m90) REVERT: C 93 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8969 (pm20) REVERT: C 96 MET cc_start: 0.9302 (mmt) cc_final: 0.8878 (mmm) REVERT: C 99 MET cc_start: 0.8984 (mtm) cc_final: 0.8462 (ptp) REVERT: C 113 GLU cc_start: 0.9456 (tt0) cc_final: 0.9210 (tm-30) REVERT: C 137 LEU cc_start: 0.9697 (mm) cc_final: 0.9433 (pp) REVERT: C 198 THR cc_start: 0.9647 (t) cc_final: 0.9446 (m) REVERT: C 201 HIS cc_start: 0.9334 (m-70) cc_final: 0.9114 (m170) REVERT: C 204 ILE cc_start: 0.9573 (mt) cc_final: 0.9288 (mt) REVERT: C 209 LYS cc_start: 0.8900 (mttt) cc_final: 0.8366 (ttmt) REVERT: C 213 CYS cc_start: 0.9276 (p) cc_final: 0.8609 (t) REVERT: C 215 MET cc_start: 0.9350 (mmp) cc_final: 0.8955 (mmm) REVERT: C 245 LYS cc_start: 0.9003 (mttt) cc_final: 0.8405 (ptpp) REVERT: C 255 MET cc_start: 0.9027 (tpt) cc_final: 0.8539 (tpp) REVERT: C 259 LEU cc_start: 0.9620 (mm) cc_final: 0.9338 (mm) REVERT: C 260 MET cc_start: 0.9669 (tpt) cc_final: 0.9379 (mmm) REVERT: C 294 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8557 (mt-10) REVERT: C 300 LYS cc_start: 0.8968 (mttt) cc_final: 0.8475 (mppt) REVERT: C 301 LYS cc_start: 0.8910 (tttt) cc_final: 0.8366 (ttpt) REVERT: C 303 GLU cc_start: 0.9231 (pt0) cc_final: 0.8879 (pp20) REVERT: C 306 GLN cc_start: 0.9014 (pt0) cc_final: 0.8696 (pm20) REVERT: C 343 PHE cc_start: 0.9528 (t80) cc_final: 0.9199 (t80) REVERT: C 347 CYS cc_start: 0.8864 (m) cc_final: 0.8321 (m) REVERT: C 403 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9022 (tp30) REVERT: C 410 MET cc_start: 0.9234 (tmm) cc_final: 0.8406 (tmm) REVERT: C 440 MET cc_start: 0.8611 (mmm) cc_final: 0.8244 (mmp) REVERT: C 463 CYS cc_start: 0.9239 (m) cc_final: 0.8835 (m) REVERT: C 483 GLN cc_start: 0.9711 (tt0) cc_final: 0.9378 (mm-40) REVERT: C 494 CYS cc_start: 0.9092 (t) cc_final: 0.8793 (p) REVERT: C 497 MET cc_start: 0.9319 (ttp) cc_final: 0.8956 (tmm) REVERT: C 538 LEU cc_start: 0.9463 (mp) cc_final: 0.9106 (mp) REVERT: C 593 TRP cc_start: 0.9224 (t60) cc_final: 0.8643 (t60) REVERT: D 35 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8865 (mt-10) REVERT: D 39 LEU cc_start: 0.9531 (tp) cc_final: 0.9286 (tp) REVERT: D 93 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9041 (pm20) REVERT: D 96 MET cc_start: 0.9267 (mmp) cc_final: 0.8935 (mmm) REVERT: D 99 MET cc_start: 0.9024 (mtm) cc_final: 0.8656 (ptp) REVERT: D 113 GLU cc_start: 0.9548 (tt0) cc_final: 0.9248 (tm-30) REVERT: D 122 HIS cc_start: 0.9591 (m170) cc_final: 0.9355 (m170) REVERT: D 136 LEU cc_start: 0.9430 (mt) cc_final: 0.9031 (mt) REVERT: D 159 LEU cc_start: 0.8784 (mm) cc_final: 0.8546 (mm) REVERT: D 198 THR cc_start: 0.9626 (t) cc_final: 0.8941 (m) REVERT: D 201 HIS cc_start: 0.9411 (m90) cc_final: 0.8931 (m90) REVERT: D 204 ILE cc_start: 0.9548 (mt) cc_final: 0.9290 (mt) REVERT: D 209 LYS cc_start: 0.8682 (mttt) cc_final: 0.8383 (mtpt) REVERT: D 215 MET cc_start: 0.9397 (mmp) cc_final: 0.8991 (mmm) REVERT: D 245 LYS cc_start: 0.8854 (mttt) cc_final: 0.8219 (ptpp) REVERT: D 246 LEU cc_start: 0.9732 (tp) cc_final: 0.9487 (tp) REVERT: D 250 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8494 (mm-30) REVERT: D 260 MET cc_start: 0.9635 (tpt) cc_final: 0.9382 (mmm) REVERT: D 300 LYS cc_start: 0.8908 (mttt) cc_final: 0.8413 (mppt) REVERT: D 301 LYS cc_start: 0.9485 (tptp) cc_final: 0.9171 (tmtt) REVERT: D 306 GLN cc_start: 0.8909 (pt0) cc_final: 0.8655 (mp10) REVERT: D 343 PHE cc_start: 0.9475 (t80) cc_final: 0.9268 (t80) REVERT: D 403 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8899 (tp30) REVERT: D 437 LEU cc_start: 0.9454 (mm) cc_final: 0.9220 (mp) REVERT: D 440 MET cc_start: 0.8236 (mmm) cc_final: 0.7878 (mmm) REVERT: D 454 MET cc_start: 0.9453 (mmt) cc_final: 0.9165 (mmt) REVERT: D 463 CYS cc_start: 0.9326 (m) cc_final: 0.9122 (m) REVERT: D 465 VAL cc_start: 0.9660 (t) cc_final: 0.9383 (m) REVERT: D 483 GLN cc_start: 0.9720 (tt0) cc_final: 0.9425 (mm-40) REVERT: D 494 CYS cc_start: 0.9167 (t) cc_final: 0.8844 (p) REVERT: D 536 LEU cc_start: 0.9768 (mt) cc_final: 0.9541 (mt) REVERT: D 537 PHE cc_start: 0.9622 (t80) cc_final: 0.9368 (t80) REVERT: D 538 LEU cc_start: 0.9527 (mp) cc_final: 0.9317 (mp) REVERT: D 542 ASP cc_start: 0.7497 (t0) cc_final: 0.6761 (t0) REVERT: D 569 LEU cc_start: 0.9796 (tp) cc_final: 0.9560 (tp) REVERT: D 593 TRP cc_start: 0.9246 (t60) cc_final: 0.8994 (t60) outliers start: 2 outliers final: 0 residues processed: 922 average time/residue: 0.2809 time to fit residues: 406.6194 Evaluate side-chains 710 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.0770 chunk 187 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 overall best weight: 2.9742 ------------------------------------------------------------------------------- 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** A 582 HIS B 265 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 596 GLN D 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20602 Z= 0.234 Angle : 0.731 8.267 27945 Z= 0.375 Chirality : 0.046 0.177 3138 Planarity : 0.005 0.064 3522 Dihedral : 7.072 102.354 2928 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 2472 helix: -0.84 (0.13), residues: 1372 sheet: -4.03 (0.57), residues: 48 loop : -2.69 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 629 HIS 0.009 0.001 HIS A 84 PHE 0.015 0.001 PHE D 468 TYR 0.018 0.002 TYR C 547 ARG 0.004 0.000 ARG C 146 *********************** 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 858 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 857 time to evaluate : 2.432 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: A 35 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8755 (mt-10) REVERT: A 39 LEU cc_start: 0.9534 (tp) cc_final: 0.9063 (tp) REVERT: A 42 LYS cc_start: 0.9398 (tttt) cc_final: 0.9060 (pptt) REVERT: A 93 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9115 (pm20) REVERT: A 113 GLU cc_start: 0.9331 (tt0) cc_final: 0.8883 (tm-30) REVERT: A 146 ARG cc_start: 0.9404 (mtt180) cc_final: 0.8935 (mmm-85) REVERT: A 215 MET cc_start: 0.9425 (mmm) cc_final: 0.8978 (mmm) REVERT: A 245 LYS cc_start: 0.8558 (mttt) cc_final: 0.7991 (mtpp) REVERT: A 255 MET cc_start: 0.9285 (mmm) cc_final: 0.8840 (tpp) REVERT: A 260 MET cc_start: 0.9619 (tpt) cc_final: 0.9303 (mmm) REVERT: A 297 ILE cc_start: 0.9526 (mm) cc_final: 0.9162 (tp) REVERT: A 300 LYS cc_start: 0.9008 (mttt) cc_final: 0.8477 (mppt) REVERT: A 306 GLN cc_start: 0.8994 (pt0) cc_final: 0.8565 (pm20) REVERT: A 343 PHE cc_start: 0.9633 (t80) cc_final: 0.9348 (t80) REVERT: A 399 ILE cc_start: 0.9280 (mt) cc_final: 0.8875 (mt) REVERT: A 403 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8915 (tp30) REVERT: A 410 MET cc_start: 0.9249 (tpt) cc_final: 0.8607 (tpp) REVERT: A 421 LEU cc_start: 0.9147 (tt) cc_final: 0.8873 (pp) REVERT: A 437 LEU cc_start: 0.9641 (mm) cc_final: 0.9380 (mp) REVERT: A 440 MET cc_start: 0.9028 (ppp) cc_final: 0.8767 (mmm) REVERT: A 454 MET cc_start: 0.9282 (mtt) cc_final: 0.8679 (tpp) REVERT: A 458 LEU cc_start: 0.9842 (mm) cc_final: 0.9535 (mm) REVERT: A 483 GLN cc_start: 0.9698 (tt0) cc_final: 0.9338 (tp-100) REVERT: A 494 CYS cc_start: 0.9203 (t) cc_final: 0.8982 (p) REVERT: A 497 MET cc_start: 0.9438 (ttp) cc_final: 0.8705 (ttp) REVERT: A 537 PHE cc_start: 0.9585 (t80) cc_final: 0.8476 (t80) REVERT: A 538 LEU cc_start: 0.9384 (mp) cc_final: 0.9140 (mp) REVERT: A 551 LEU cc_start: 0.8133 (mt) cc_final: 0.7918 (mp) REVERT: A 570 MET cc_start: 0.9251 (mmp) cc_final: 0.9014 (mmm) REVERT: A 580 ASP cc_start: 0.8727 (m-30) cc_final: 0.8313 (m-30) REVERT: B 50 LEU cc_start: 0.9308 (mm) cc_final: 0.8538 (tp) REVERT: B 57 ASP cc_start: 0.9031 (m-30) cc_final: 0.8803 (m-30) REVERT: B 70 CYS cc_start: 0.8726 (p) cc_final: 0.7967 (p) REVERT: B 93 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8946 (pm20) REVERT: B 96 MET cc_start: 0.9599 (mmt) cc_final: 0.9216 (mmp) REVERT: B 99 MET cc_start: 0.9429 (mtm) cc_final: 0.8939 (ptp) REVERT: B 113 GLU cc_start: 0.9486 (tt0) cc_final: 0.9132 (tm-30) REVERT: B 118 GLN cc_start: 0.9420 (tt0) cc_final: 0.8915 (tm-30) REVERT: B 128 GLN cc_start: 0.9148 (pt0) cc_final: 0.8374 (tm-30) REVERT: B 174 ASN cc_start: 0.8889 (t0) cc_final: 0.8571 (t0) REVERT: B 209 LYS cc_start: 0.9283 (mttt) cc_final: 0.8736 (ttmt) REVERT: B 245 LYS cc_start: 0.9430 (mttt) cc_final: 0.9052 (ptpp) REVERT: B 246 LEU cc_start: 0.9633 (tp) cc_final: 0.9411 (tp) REVERT: B 260 MET cc_start: 0.9596 (mmm) cc_final: 0.9159 (mmm) REVERT: B 300 LYS cc_start: 0.8963 (mttt) cc_final: 0.8537 (mppt) REVERT: B 303 GLU cc_start: 0.9080 (tp30) cc_final: 0.8455 (tp30) REVERT: B 306 GLN cc_start: 0.8964 (pt0) cc_final: 0.8471 (pm20) REVERT: B 403 GLU cc_start: 0.8956 (tp30) cc_final: 0.8717 (tp30) REVERT: B 454 MET cc_start: 0.9579 (mmt) cc_final: 0.8893 (tpp) REVERT: B 463 CYS cc_start: 0.9301 (m) cc_final: 0.8950 (m) REVERT: B 483 GLN cc_start: 0.9701 (tt0) cc_final: 0.9424 (tt0) REVERT: B 494 CYS cc_start: 0.9001 (t) cc_final: 0.8755 (p) REVERT: B 497 MET cc_start: 0.9278 (ttp) cc_final: 0.8693 (ttp) REVERT: B 528 MET cc_start: 0.8347 (mmp) cc_final: 0.7533 (mmm) REVERT: B 537 PHE cc_start: 0.9459 (t80) cc_final: 0.8221 (t80) REVERT: B 538 LEU cc_start: 0.9239 (mp) cc_final: 0.8672 (mp) REVERT: B 541 ILE cc_start: 0.8889 (pt) cc_final: 0.8536 (pt) REVERT: B 551 LEU cc_start: 0.8970 (mt) cc_final: 0.8761 (mp) REVERT: C 35 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8933 (mp0) REVERT: C 84 HIS cc_start: 0.9168 (m90) cc_final: 0.8807 (m90) REVERT: C 93 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8995 (pm20) REVERT: C 96 MET cc_start: 0.9348 (mmt) cc_final: 0.8872 (mmm) REVERT: C 99 MET cc_start: 0.9037 (mtm) cc_final: 0.8492 (ptp) REVERT: C 137 LEU cc_start: 0.9705 (mm) cc_final: 0.9453 (pp) REVERT: C 204 ILE cc_start: 0.9619 (mt) cc_final: 0.9339 (mt) REVERT: C 206 GLN cc_start: 0.9392 (mm-40) cc_final: 0.8943 (mm110) REVERT: C 209 LYS cc_start: 0.8839 (mttt) cc_final: 0.8206 (ttmt) REVERT: C 215 MET cc_start: 0.9354 (mmp) cc_final: 0.9098 (mmm) REVERT: C 245 LYS cc_start: 0.9027 (mttt) cc_final: 0.8442 (ptpp) REVERT: C 246 LEU cc_start: 0.9700 (tp) cc_final: 0.9455 (tp) REVERT: C 250 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8736 (mm-30) REVERT: C 259 LEU cc_start: 0.9584 (mm) cc_final: 0.9268 (mm) REVERT: C 260 MET cc_start: 0.9694 (tpt) cc_final: 0.9369 (mmm) REVERT: C 294 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8574 (mt-10) REVERT: C 300 LYS cc_start: 0.9059 (mttt) cc_final: 0.8582 (mppt) REVERT: C 301 LYS cc_start: 0.8893 (tttt) cc_final: 0.8475 (ttpt) REVERT: C 303 GLU cc_start: 0.9215 (pt0) cc_final: 0.8899 (pp20) REVERT: C 306 GLN cc_start: 0.9049 (pt0) cc_final: 0.8714 (pm20) REVERT: C 372 LEU cc_start: 0.9459 (pp) cc_final: 0.8626 (pt) REVERT: C 403 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8954 (tp30) REVERT: C 440 MET cc_start: 0.8687 (mmm) cc_final: 0.8325 (mmp) REVERT: C 485 MET cc_start: 0.9712 (mtp) cc_final: 0.9425 (mmm) REVERT: C 497 MET cc_start: 0.9415 (ttp) cc_final: 0.8719 (tmm) REVERT: C 518 GLU cc_start: 0.8782 (mp0) cc_final: 0.8466 (mp0) REVERT: C 534 PHE cc_start: 0.8918 (t80) cc_final: 0.8706 (t80) REVERT: C 537 PHE cc_start: 0.9581 (t80) cc_final: 0.9267 (t80) REVERT: C 538 LEU cc_start: 0.9336 (mp) cc_final: 0.8971 (mp) REVERT: C 570 MET cc_start: 0.9251 (mmp) cc_final: 0.8996 (mmm) REVERT: C 577 MET cc_start: 0.9013 (ppp) cc_final: 0.8796 (ppp) REVERT: C 593 TRP cc_start: 0.9289 (t60) cc_final: 0.8869 (t60) REVERT: D 35 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8870 (mt-10) REVERT: D 93 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9024 (pm20) REVERT: D 96 MET cc_start: 0.9341 (mmp) cc_final: 0.8848 (mmp) REVERT: D 99 MET cc_start: 0.9088 (mtm) cc_final: 0.8746 (ptp) REVERT: D 113 GLU cc_start: 0.9543 (tt0) cc_final: 0.9248 (tm-30) REVERT: D 161 TYR cc_start: 0.8687 (t80) cc_final: 0.8215 (t80) REVERT: D 198 THR cc_start: 0.9649 (t) cc_final: 0.9417 (m) REVERT: D 204 ILE cc_start: 0.9610 (mt) cc_final: 0.9336 (mt) REVERT: D 206 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9011 (mm110) REVERT: D 209 LYS cc_start: 0.8834 (mttt) cc_final: 0.8219 (mtpt) REVERT: D 215 MET cc_start: 0.9382 (mmp) cc_final: 0.8940 (mmm) REVERT: D 245 LYS cc_start: 0.8929 (mttt) cc_final: 0.8335 (ptpp) REVERT: D 246 LEU cc_start: 0.9734 (tp) cc_final: 0.9492 (tp) REVERT: D 250 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8496 (mm-30) REVERT: D 255 MET cc_start: 0.9219 (tpp) cc_final: 0.8915 (tpp) REVERT: D 260 MET cc_start: 0.9659 (tpt) cc_final: 0.9350 (mmm) REVERT: D 297 ILE cc_start: 0.9407 (pt) cc_final: 0.9171 (tp) REVERT: D 300 LYS cc_start: 0.8938 (mttt) cc_final: 0.8448 (mppt) REVERT: D 301 LYS cc_start: 0.9470 (tptp) cc_final: 0.9086 (tmtt) REVERT: D 303 GLU cc_start: 0.9229 (tp30) cc_final: 0.8938 (tp30) REVERT: D 306 GLN cc_start: 0.8950 (pt0) cc_final: 0.8654 (pm20) REVERT: D 403 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8898 (tp30) REVERT: D 410 MET cc_start: 0.9284 (tpt) cc_final: 0.8612 (tpp) REVERT: D 421 LEU cc_start: 0.9361 (tp) cc_final: 0.8903 (tp) REVERT: D 440 MET cc_start: 0.8242 (mmm) cc_final: 0.7809 (mmm) REVERT: D 454 MET cc_start: 0.9442 (mmt) cc_final: 0.9167 (mmt) REVERT: D 463 CYS cc_start: 0.9335 (m) cc_final: 0.9108 (m) REVERT: D 494 CYS cc_start: 0.9155 (t) cc_final: 0.8835 (p) REVERT: D 536 LEU cc_start: 0.9764 (mt) cc_final: 0.9526 (mt) REVERT: D 538 LEU cc_start: 0.9413 (mp) cc_final: 0.9069 (mp) REVERT: D 570 MET cc_start: 0.9258 (mmp) cc_final: 0.8930 (mmm) REVERT: D 593 TRP cc_start: 0.9295 (t60) cc_final: 0.8580 (t60) outliers start: 1 outliers final: 0 residues processed: 857 average time/residue: 0.2753 time to fit residues: 373.2165 Evaluate side-chains 684 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.0670 chunk 169 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.0050 chunk 151 optimal weight: 0.6980 chunk 226 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 0.0040 chunk 64 optimal weight: 2.9990 overall best weight: 0.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN D 84 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20602 Z= 0.172 Angle : 0.706 7.528 27945 Z= 0.349 Chirality : 0.044 0.180 3138 Planarity : 0.005 0.062 3522 Dihedral : 6.455 94.161 2928 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2472 helix: -0.45 (0.14), residues: 1364 sheet: -4.06 (0.58), residues: 48 loop : -2.59 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 268 HIS 0.006 0.001 HIS B 522 PHE 0.020 0.001 PHE D 468 TYR 0.012 0.001 TYR A 526 ARG 0.006 0.000 ARG A 139 *********************** 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 893 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 893 time to evaluate : 2.189 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 39 LEU cc_start: 0.9556 (tp) cc_final: 0.9111 (tp) REVERT: A 42 LYS cc_start: 0.9356 (tttt) cc_final: 0.8987 (pptt) REVERT: A 84 HIS cc_start: 0.9326 (m90) cc_final: 0.9096 (m170) REVERT: A 93 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8968 (pm20) REVERT: A 113 GLU cc_start: 0.9337 (tt0) cc_final: 0.8871 (tm-30) REVERT: A 146 ARG cc_start: 0.9418 (mtt180) cc_final: 0.8949 (mmm-85) REVERT: A 206 GLN cc_start: 0.9468 (mm-40) cc_final: 0.8931 (mm-40) REVERT: A 215 MET cc_start: 0.9417 (mmm) cc_final: 0.8995 (mmm) REVERT: A 245 LYS cc_start: 0.8470 (mttt) cc_final: 0.8191 (mtpt) REVERT: A 255 MET cc_start: 0.9139 (mmm) cc_final: 0.8669 (tpp) REVERT: A 260 MET cc_start: 0.9616 (tpt) cc_final: 0.9269 (mmm) REVERT: A 297 ILE cc_start: 0.9507 (mm) cc_final: 0.9256 (tp) REVERT: A 300 LYS cc_start: 0.9049 (mttt) cc_final: 0.8528 (mppt) REVERT: A 301 LYS cc_start: 0.9435 (tptt) cc_final: 0.9022 (tmtt) REVERT: A 306 GLN cc_start: 0.8852 (pt0) cc_final: 0.8545 (pm20) REVERT: A 345 MET cc_start: 0.8282 (ptm) cc_final: 0.8040 (ppp) REVERT: A 399 ILE cc_start: 0.9244 (mt) cc_final: 0.8815 (mt) REVERT: A 403 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8875 (tp30) REVERT: A 410 MET cc_start: 0.9222 (tpt) cc_final: 0.8200 (tpp) REVERT: A 437 LEU cc_start: 0.9624 (mm) cc_final: 0.9340 (mt) REVERT: A 440 MET cc_start: 0.9017 (ppp) cc_final: 0.8777 (tpt) REVERT: A 454 MET cc_start: 0.9201 (mtt) cc_final: 0.8889 (mmm) REVERT: A 463 CYS cc_start: 0.9283 (m) cc_final: 0.9033 (m) REVERT: A 466 MET cc_start: 0.9712 (mtt) cc_final: 0.9505 (mmt) REVERT: A 483 GLN cc_start: 0.9650 (tt0) cc_final: 0.9264 (tp-100) REVERT: A 491 MET cc_start: 0.9037 (ttt) cc_final: 0.8600 (ttm) REVERT: A 494 CYS cc_start: 0.9138 (t) cc_final: 0.8932 (p) REVERT: A 497 MET cc_start: 0.9474 (ttp) cc_final: 0.8731 (ttp) REVERT: A 515 GLU cc_start: 0.9157 (tp30) cc_final: 0.8694 (tp30) REVERT: A 537 PHE cc_start: 0.9584 (t80) cc_final: 0.8357 (t80) REVERT: A 538 LEU cc_start: 0.9298 (mp) cc_final: 0.9043 (mp) REVERT: A 541 ILE cc_start: 0.8951 (pt) cc_final: 0.8276 (mm) REVERT: A 570 MET cc_start: 0.9291 (mmp) cc_final: 0.9044 (mmm) REVERT: A 577 MET cc_start: 0.9124 (mmt) cc_final: 0.8488 (mmm) REVERT: A 580 ASP cc_start: 0.8474 (m-30) cc_final: 0.7886 (m-30) REVERT: A 605 GLU cc_start: 0.9270 (tt0) cc_final: 0.9024 (tt0) REVERT: B 57 ASP cc_start: 0.9076 (m-30) cc_final: 0.8793 (m-30) REVERT: B 70 CYS cc_start: 0.8729 (p) cc_final: 0.8129 (p) REVERT: B 78 MET cc_start: 0.7067 (ptt) cc_final: 0.6822 (ptp) REVERT: B 93 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8913 (pm20) REVERT: B 96 MET cc_start: 0.9579 (mmt) cc_final: 0.9292 (mmm) REVERT: B 98 LEU cc_start: 0.9638 (mt) cc_final: 0.9327 (pp) REVERT: B 99 MET cc_start: 0.9364 (mtm) cc_final: 0.8747 (tpp) REVERT: B 113 GLU cc_start: 0.9509 (tt0) cc_final: 0.9125 (tm-30) REVERT: B 118 GLN cc_start: 0.9409 (tt0) cc_final: 0.8900 (tm-30) REVERT: B 123 ILE cc_start: 0.9594 (mt) cc_final: 0.9263 (mt) REVERT: B 128 GLN cc_start: 0.9027 (pt0) cc_final: 0.8279 (tm-30) REVERT: B 174 ASN cc_start: 0.8887 (t0) cc_final: 0.8626 (t0) REVERT: B 181 LEU cc_start: 0.9689 (tp) cc_final: 0.9420 (pp) REVERT: B 182 LEU cc_start: 0.9748 (mm) cc_final: 0.9462 (mm) REVERT: B 204 ILE cc_start: 0.9535 (mt) cc_final: 0.9287 (tp) REVERT: B 209 LYS cc_start: 0.9241 (mttt) cc_final: 0.8641 (ttmt) REVERT: B 245 LYS cc_start: 0.9369 (mttt) cc_final: 0.8856 (ptpp) REVERT: B 246 LEU cc_start: 0.9648 (tp) cc_final: 0.9425 (tp) REVERT: B 255 MET cc_start: 0.9331 (tpp) cc_final: 0.9068 (tpp) REVERT: B 259 LEU cc_start: 0.9708 (mm) cc_final: 0.9451 (mm) REVERT: B 260 MET cc_start: 0.9586 (mmm) cc_final: 0.9127 (mmm) REVERT: B 294 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8754 (mt-10) REVERT: B 297 ILE cc_start: 0.9518 (pt) cc_final: 0.9222 (tp) REVERT: B 300 LYS cc_start: 0.8929 (mttt) cc_final: 0.8501 (mppt) REVERT: B 303 GLU cc_start: 0.9049 (tp30) cc_final: 0.8419 (tp30) REVERT: B 306 GLN cc_start: 0.8912 (pt0) cc_final: 0.8386 (pm20) REVERT: B 320 LYS cc_start: 0.9388 (pttt) cc_final: 0.9158 (ptpt) REVERT: B 331 MET cc_start: 0.7405 (tmm) cc_final: 0.7157 (tmm) REVERT: B 403 GLU cc_start: 0.8985 (tp30) cc_final: 0.8718 (tp30) REVERT: B 410 MET cc_start: 0.8841 (tmm) cc_final: 0.8553 (tmm) REVERT: B 421 LEU cc_start: 0.9296 (tt) cc_final: 0.8802 (tt) REVERT: B 454 MET cc_start: 0.9458 (mmt) cc_final: 0.8797 (tpp) REVERT: B 463 CYS cc_start: 0.9264 (m) cc_final: 0.9018 (m) REVERT: B 483 GLN cc_start: 0.9680 (tt0) cc_final: 0.9334 (tp40) REVERT: B 491 MET cc_start: 0.8950 (ttt) cc_final: 0.8688 (ttt) REVERT: B 494 CYS cc_start: 0.9004 (t) cc_final: 0.8795 (p) REVERT: B 497 MET cc_start: 0.9277 (ttp) cc_final: 0.8600 (ttp) REVERT: B 513 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8990 (tp40) REVERT: B 518 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8966 (mp0) REVERT: B 528 MET cc_start: 0.8249 (mmp) cc_final: 0.7473 (tpp) REVERT: B 537 PHE cc_start: 0.9437 (t80) cc_final: 0.8109 (t80) REVERT: B 538 LEU cc_start: 0.9147 (mp) cc_final: 0.8617 (mp) REVERT: B 541 ILE cc_start: 0.8892 (pt) cc_final: 0.8580 (pt) REVERT: B 542 ASP cc_start: 0.7832 (m-30) cc_final: 0.7607 (m-30) REVERT: B 569 LEU cc_start: 0.9841 (tp) cc_final: 0.9627 (tp) REVERT: B 574 LEU cc_start: 0.9817 (tp) cc_final: 0.9487 (tp) REVERT: B 592 LEU cc_start: 0.9494 (mm) cc_final: 0.9248 (mm) REVERT: B 605 GLU cc_start: 0.9049 (tt0) cc_final: 0.8739 (tt0) REVERT: C 34 ASP cc_start: 0.9546 (m-30) cc_final: 0.9284 (m-30) REVERT: C 35 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8850 (mp0) REVERT: C 84 HIS cc_start: 0.9152 (m90) cc_final: 0.8726 (m90) REVERT: C 93 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8931 (pm20) REVERT: C 96 MET cc_start: 0.9298 (mmt) cc_final: 0.8894 (mmm) REVERT: C 99 MET cc_start: 0.8991 (mtm) cc_final: 0.8547 (ptp) REVERT: C 204 ILE cc_start: 0.9604 (mt) cc_final: 0.9343 (mt) REVERT: C 206 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8744 (mm-40) REVERT: C 209 LYS cc_start: 0.8807 (mttt) cc_final: 0.8150 (ttmt) REVERT: C 215 MET cc_start: 0.9394 (mmp) cc_final: 0.8899 (mmm) REVERT: C 230 GLN cc_start: 0.8642 (mt0) cc_final: 0.8335 (mt0) REVERT: C 245 LYS cc_start: 0.8994 (mttt) cc_final: 0.8341 (ptpp) REVERT: C 246 LEU cc_start: 0.9705 (tp) cc_final: 0.9420 (tp) REVERT: C 250 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8679 (mm-30) REVERT: C 255 MET cc_start: 0.9374 (tpp) cc_final: 0.9121 (tpp) REVERT: C 259 LEU cc_start: 0.9626 (mm) cc_final: 0.9372 (mm) REVERT: C 260 MET cc_start: 0.9669 (tpt) cc_final: 0.9350 (mmm) REVERT: C 294 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 300 LYS cc_start: 0.9047 (mttt) cc_final: 0.8573 (mppt) REVERT: C 301 LYS cc_start: 0.8894 (tttt) cc_final: 0.8377 (ttpt) REVERT: C 303 GLU cc_start: 0.9157 (pt0) cc_final: 0.8819 (pp20) REVERT: C 306 GLN cc_start: 0.9025 (pt0) cc_final: 0.8714 (pm20) REVERT: C 403 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8945 (tp30) REVERT: C 440 MET cc_start: 0.8675 (mmm) cc_final: 0.8268 (mmp) REVERT: C 458 LEU cc_start: 0.9802 (mm) cc_final: 0.9583 (mm) REVERT: C 485 MET cc_start: 0.9708 (mtp) cc_final: 0.9426 (mmm) REVERT: C 526 TYR cc_start: 0.8886 (t80) cc_final: 0.8673 (t80) REVERT: C 538 LEU cc_start: 0.9270 (mp) cc_final: 0.8684 (mp) REVERT: C 593 TRP cc_start: 0.9272 (t60) cc_final: 0.8862 (t60) REVERT: D 35 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8826 (mt-10) REVERT: D 39 LEU cc_start: 0.9443 (tp) cc_final: 0.9231 (tp) REVERT: D 84 HIS cc_start: 0.9026 (m90) cc_final: 0.8727 (m90) REVERT: D 93 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8984 (pm20) REVERT: D 96 MET cc_start: 0.9333 (mmp) cc_final: 0.8867 (mmp) REVERT: D 99 MET cc_start: 0.9012 (mtm) cc_final: 0.8716 (ptp) REVERT: D 113 GLU cc_start: 0.9551 (tt0) cc_final: 0.9262 (tm-30) REVERT: D 123 ILE cc_start: 0.9696 (tt) cc_final: 0.9492 (mp) REVERT: D 161 TYR cc_start: 0.8342 (t80) cc_final: 0.8108 (t80) REVERT: D 198 THR cc_start: 0.9608 (t) cc_final: 0.9405 (m) REVERT: D 204 ILE cc_start: 0.9590 (mt) cc_final: 0.9357 (mt) REVERT: D 206 GLN cc_start: 0.9458 (mm-40) cc_final: 0.8914 (mm-40) REVERT: D 209 LYS cc_start: 0.8709 (mttt) cc_final: 0.8046 (ttmt) REVERT: D 215 MET cc_start: 0.9337 (mmp) cc_final: 0.8929 (mmm) REVERT: D 245 LYS cc_start: 0.8706 (mttt) cc_final: 0.8085 (ptpp) REVERT: D 246 LEU cc_start: 0.9704 (tp) cc_final: 0.9438 (tp) REVERT: D 250 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8450 (mm-30) REVERT: D 260 MET cc_start: 0.9646 (tpt) cc_final: 0.9317 (mmm) REVERT: D 300 LYS cc_start: 0.8995 (mttt) cc_final: 0.8507 (mppt) REVERT: D 301 LYS cc_start: 0.9445 (tptp) cc_final: 0.7979 (tmtt) REVERT: D 343 PHE cc_start: 0.9552 (t80) cc_final: 0.9294 (t80) REVERT: D 347 CYS cc_start: 0.8593 (m) cc_final: 0.8274 (m) REVERT: D 367 LEU cc_start: 0.9248 (tp) cc_final: 0.8987 (tp) REVERT: D 399 ILE cc_start: 0.8362 (mm) cc_final: 0.8057 (mm) REVERT: D 403 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8796 (tp30) REVERT: D 410 MET cc_start: 0.9293 (tpt) cc_final: 0.8600 (tpp) REVERT: D 421 LEU cc_start: 0.9360 (tp) cc_final: 0.8859 (tp) REVERT: D 442 MET cc_start: 0.9568 (ptm) cc_final: 0.9231 (tmm) REVERT: D 454 MET cc_start: 0.9342 (mmt) cc_final: 0.8947 (mmt) REVERT: D 463 CYS cc_start: 0.9331 (m) cc_final: 0.8985 (m) REVERT: D 483 GLN cc_start: 0.9708 (tt0) cc_final: 0.9356 (tp-100) REVERT: D 491 MET cc_start: 0.8804 (ttt) cc_final: 0.8553 (ttm) REVERT: D 494 CYS cc_start: 0.9139 (t) cc_final: 0.8877 (p) REVERT: D 497 MET cc_start: 0.8902 (tmm) cc_final: 0.8608 (tmm) REVERT: D 518 GLU cc_start: 0.8945 (mp0) cc_final: 0.8741 (mp0) REVERT: D 526 TYR cc_start: 0.8885 (t80) cc_final: 0.8677 (t80) REVERT: D 536 LEU cc_start: 0.9743 (mt) cc_final: 0.9533 (mt) REVERT: D 570 MET cc_start: 0.9260 (mmp) cc_final: 0.8998 (mmm) outliers start: 0 outliers final: 0 residues processed: 893 average time/residue: 0.2710 time to fit residues: 382.9029 Evaluate side-chains 701 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 122 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 2.6384 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 74 GLN D 267 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4712 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= 0.216 Angle : 0.710 8.097 27945 Z= 0.360 Chirality : 0.045 0.184 3138 Planarity : 0.004 0.057 3522 Dihedral : 6.216 85.652 2928 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2472 helix: -0.20 (0.14), residues: 1356 sheet: -4.07 (0.57), residues: 48 loop : -2.50 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 268 HIS 0.009 0.001 HIS C 84 PHE 0.017 0.001 PHE D 537 TYR 0.016 0.001 TYR C 161 ARG 0.005 0.000 ARG A 75 *********************** 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 804 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 803 time to evaluate : 2.000 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: 0.9042 (mt-10) cc_final: 0.8786 (mt-10) REVERT: A 39 LEU cc_start: 0.9578 (tp) cc_final: 0.9142 (tp) REVERT: A 40 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8493 (tp40) REVERT: A 42 LYS cc_start: 0.9349 (tttt) cc_final: 0.9048 (pttt) REVERT: A 93 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8845 (pm20) REVERT: A 113 GLU cc_start: 0.9376 (tt0) cc_final: 0.8921 (tm-30) REVERT: A 146 ARG cc_start: 0.9466 (mtt180) cc_final: 0.9010 (mmm-85) REVERT: A 182 LEU cc_start: 0.9742 (mm) cc_final: 0.9406 (mm) REVERT: A 206 GLN cc_start: 0.9467 (mm-40) cc_final: 0.9059 (mm110) REVERT: A 209 LYS cc_start: 0.8429 (mttt) cc_final: 0.8066 (ttmt) REVERT: A 215 MET cc_start: 0.9402 (mmm) cc_final: 0.8991 (mmm) REVERT: A 245 LYS cc_start: 0.8567 (mttt) cc_final: 0.8290 (mttm) REVERT: A 260 MET cc_start: 0.9650 (tpt) cc_final: 0.9303 (mmm) REVERT: A 297 ILE cc_start: 0.9457 (mm) cc_final: 0.9201 (tp) REVERT: A 300 LYS cc_start: 0.9140 (mttt) cc_final: 0.8629 (mppt) REVERT: A 306 GLN cc_start: 0.8940 (pt0) cc_final: 0.8656 (mp10) REVERT: A 343 PHE cc_start: 0.9649 (t80) cc_final: 0.9396 (t80) REVERT: A 345 MET cc_start: 0.8411 (ptm) cc_final: 0.8185 (ppp) REVERT: A 403 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8908 (tp30) REVERT: A 410 MET cc_start: 0.9091 (tpt) cc_final: 0.8424 (tpp) REVERT: A 435 MET cc_start: 0.8875 (mmt) cc_final: 0.8609 (mmp) REVERT: A 454 MET cc_start: 0.9273 (mtt) cc_final: 0.8673 (tpp) REVERT: A 458 LEU cc_start: 0.9843 (mm) cc_final: 0.9628 (mm) REVERT: A 483 GLN cc_start: 0.9661 (tt0) cc_final: 0.9284 (tp-100) REVERT: A 491 MET cc_start: 0.9165 (ttt) cc_final: 0.8837 (ttm) REVERT: A 494 CYS cc_start: 0.9157 (t) cc_final: 0.8913 (p) REVERT: A 497 MET cc_start: 0.9507 (ttp) cc_final: 0.8872 (ttp) REVERT: A 515 GLU cc_start: 0.9169 (tp30) cc_final: 0.8656 (tp30) REVERT: A 537 PHE cc_start: 0.9583 (t80) cc_final: 0.8512 (t80) REVERT: A 538 LEU cc_start: 0.9292 (mp) cc_final: 0.9077 (mp) REVERT: A 541 ILE cc_start: 0.8941 (pt) cc_final: 0.8332 (mm) REVERT: A 570 MET cc_start: 0.9441 (mmp) cc_final: 0.9119 (mmm) REVERT: A 577 MET cc_start: 0.9070 (mmt) cc_final: 0.8756 (mmm) REVERT: A 580 ASP cc_start: 0.8581 (m-30) cc_final: 0.7954 (m-30) REVERT: A 605 GLU cc_start: 0.9349 (tt0) cc_final: 0.9106 (tt0) REVERT: B 57 ASP cc_start: 0.9084 (m-30) cc_final: 0.8703 (m-30) REVERT: B 70 CYS cc_start: 0.8483 (p) cc_final: 0.7928 (p) REVERT: B 93 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8943 (pm20) REVERT: B 96 MET cc_start: 0.9604 (mmt) cc_final: 0.9310 (mmm) REVERT: B 113 GLU cc_start: 0.9495 (tt0) cc_final: 0.9124 (tm-30) REVERT: B 118 GLN cc_start: 0.9460 (tt0) cc_final: 0.8991 (tm-30) REVERT: B 123 ILE cc_start: 0.9602 (mt) cc_final: 0.9258 (mt) REVERT: B 128 GLN cc_start: 0.9222 (pt0) cc_final: 0.8374 (tm-30) REVERT: B 181 LEU cc_start: 0.9727 (tp) cc_final: 0.9413 (pp) REVERT: B 182 LEU cc_start: 0.9784 (mm) cc_final: 0.9495 (mm) REVERT: B 209 LYS cc_start: 0.9225 (mttt) cc_final: 0.8695 (ttmt) REVERT: B 215 MET cc_start: 0.9585 (tmm) cc_final: 0.9213 (tmm) REVERT: B 245 LYS cc_start: 0.9353 (mttt) cc_final: 0.8789 (ptpp) REVERT: B 246 LEU cc_start: 0.9673 (tp) cc_final: 0.9462 (tp) REVERT: B 260 MET cc_start: 0.9586 (mmm) cc_final: 0.9131 (mmm) REVERT: B 293 LEU cc_start: 0.9775 (mt) cc_final: 0.9514 (pp) REVERT: B 294 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 300 LYS cc_start: 0.8941 (mttt) cc_final: 0.8402 (mppt) REVERT: B 303 GLU cc_start: 0.9055 (tp30) cc_final: 0.8360 (tp30) REVERT: B 306 GLN cc_start: 0.8993 (pt0) cc_final: 0.8542 (pm20) REVERT: B 403 GLU cc_start: 0.9014 (tp30) cc_final: 0.8770 (tp30) REVERT: B 454 MET cc_start: 0.9439 (mmt) cc_final: 0.8816 (tpp) REVERT: B 463 CYS cc_start: 0.9404 (m) cc_final: 0.9187 (m) REVERT: B 483 GLN cc_start: 0.9684 (tt0) cc_final: 0.9344 (tp40) REVERT: B 491 MET cc_start: 0.8958 (ttt) cc_final: 0.8554 (ttm) REVERT: B 494 CYS cc_start: 0.9080 (t) cc_final: 0.8867 (p) REVERT: B 497 MET cc_start: 0.9337 (ttp) cc_final: 0.8704 (ttp) REVERT: B 513 GLN cc_start: 0.9463 (tp-100) cc_final: 0.8976 (tp40) REVERT: B 528 MET cc_start: 0.8281 (mmp) cc_final: 0.7845 (tpp) REVERT: B 537 PHE cc_start: 0.9472 (t80) cc_final: 0.8271 (t80) REVERT: B 538 LEU cc_start: 0.9202 (mp) cc_final: 0.8926 (mp) REVERT: B 541 ILE cc_start: 0.9052 (pt) cc_final: 0.8790 (pt) REVERT: B 569 LEU cc_start: 0.9834 (tp) cc_final: 0.9619 (tp) REVERT: B 570 MET cc_start: 0.9428 (mmm) cc_final: 0.9152 (mmm) REVERT: B 574 LEU cc_start: 0.9807 (tp) cc_final: 0.9520 (tp) REVERT: C 35 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8905 (mp0) REVERT: C 93 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8843 (pm20) REVERT: C 96 MET cc_start: 0.9334 (mmt) cc_final: 0.8917 (tmm) REVERT: C 110 MET cc_start: 0.9224 (mmm) cc_final: 0.8838 (mmm) REVERT: C 137 LEU cc_start: 0.9637 (mt) cc_final: 0.9402 (pp) REVERT: C 204 ILE cc_start: 0.9653 (mt) cc_final: 0.9411 (mt) REVERT: C 206 GLN cc_start: 0.9399 (mm-40) cc_final: 0.8843 (mm-40) REVERT: C 209 LYS cc_start: 0.8849 (mttt) cc_final: 0.8163 (ttmt) REVERT: C 215 MET cc_start: 0.9394 (mmp) cc_final: 0.9017 (mmm) REVERT: C 245 LYS cc_start: 0.9030 (mttt) cc_final: 0.8439 (ptpp) REVERT: C 246 LEU cc_start: 0.9715 (tp) cc_final: 0.9435 (tp) REVERT: C 250 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8500 (mm-30) REVERT: C 255 MET cc_start: 0.9435 (tpp) cc_final: 0.9226 (tpp) REVERT: C 259 LEU cc_start: 0.9589 (mm) cc_final: 0.9375 (mm) REVERT: C 260 MET cc_start: 0.9677 (tpt) cc_final: 0.9379 (mmm) REVERT: C 294 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8622 (mt-10) REVERT: C 297 ILE cc_start: 0.9506 (tp) cc_final: 0.9285 (tp) REVERT: C 300 LYS cc_start: 0.9120 (mttt) cc_final: 0.8672 (mppt) REVERT: C 306 GLN cc_start: 0.9071 (pt0) cc_final: 0.8593 (mp10) REVERT: C 403 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8938 (tp30) REVERT: C 450 GLU cc_start: 0.9517 (pm20) cc_final: 0.9079 (pm20) REVERT: C 454 MET cc_start: 0.9186 (tpp) cc_final: 0.8544 (tpp) REVERT: C 458 LEU cc_start: 0.9850 (mm) cc_final: 0.9543 (mm) REVERT: C 518 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8917 (tm-30) REVERT: C 526 TYR cc_start: 0.8975 (t80) cc_final: 0.8767 (t80) REVERT: C 536 LEU cc_start: 0.9726 (mt) cc_final: 0.9507 (mt) REVERT: C 570 MET cc_start: 0.9411 (mmp) cc_final: 0.9178 (mmm) REVERT: C 593 TRP cc_start: 0.9288 (t60) cc_final: 0.8924 (t60) REVERT: D 35 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8889 (mt-10) REVERT: D 93 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8952 (pm20) REVERT: D 96 MET cc_start: 0.9408 (mmp) cc_final: 0.8939 (mmp) REVERT: D 99 MET cc_start: 0.9057 (mtm) cc_final: 0.8700 (ptp) REVERT: D 113 GLU cc_start: 0.9576 (tt0) cc_final: 0.9296 (tm-30) REVERT: D 204 ILE cc_start: 0.9602 (mt) cc_final: 0.9373 (mt) REVERT: D 206 GLN cc_start: 0.9490 (mm-40) cc_final: 0.8961 (mm-40) REVERT: D 209 LYS cc_start: 0.8751 (mttt) cc_final: 0.8153 (ttmt) REVERT: D 215 MET cc_start: 0.9365 (mmp) cc_final: 0.8927 (mmm) REVERT: D 245 LYS cc_start: 0.9050 (mttt) cc_final: 0.8425 (ptpp) REVERT: D 246 LEU cc_start: 0.9701 (tp) cc_final: 0.9447 (tp) REVERT: D 250 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8522 (mm-30) REVERT: D 260 MET cc_start: 0.9674 (tpt) cc_final: 0.9305 (mmm) REVERT: D 300 LYS cc_start: 0.8976 (mttt) cc_final: 0.8557 (mppt) REVERT: D 343 PHE cc_start: 0.9587 (t80) cc_final: 0.9309 (t80) REVERT: D 347 CYS cc_start: 0.8623 (m) cc_final: 0.8364 (m) REVERT: D 367 LEU cc_start: 0.9191 (tp) cc_final: 0.8733 (tp) REVERT: D 403 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8838 (tp30) REVERT: D 442 MET cc_start: 0.9586 (ptm) cc_final: 0.9283 (tmm) REVERT: D 454 MET cc_start: 0.9404 (mmt) cc_final: 0.9148 (mmm) REVERT: D 483 GLN cc_start: 0.9709 (tt0) cc_final: 0.9387 (tt0) REVERT: D 491 MET cc_start: 0.8852 (ttt) cc_final: 0.8621 (ttm) REVERT: D 497 MET cc_start: 0.8903 (tmm) cc_final: 0.8685 (tmm) REVERT: D 518 GLU cc_start: 0.8998 (mp0) cc_final: 0.8778 (mp0) REVERT: D 526 TYR cc_start: 0.8902 (t80) cc_final: 0.8677 (t80) REVERT: D 536 LEU cc_start: 0.9753 (mt) cc_final: 0.9550 (mt) REVERT: D 570 MET cc_start: 0.9344 (mmp) cc_final: 0.9029 (mmm) outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.2853 time to fit residues: 366.2636 Evaluate side-chains 678 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 0.0570 chunk 125 optimal weight: 10.0000 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN D 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20602 Z= 0.166 Angle : 0.716 15.599 27945 Z= 0.350 Chirality : 0.044 0.182 3138 Planarity : 0.004 0.058 3522 Dihedral : 5.756 71.061 2928 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2472 helix: -0.24 (0.14), residues: 1428 sheet: -3.65 (0.45), residues: 64 loop : -2.59 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 268 HIS 0.008 0.001 HIS A 84 PHE 0.019 0.001 PHE C 468 TYR 0.012 0.001 TYR A 526 ARG 0.006 0.000 ARG A 139 *********************** 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 823 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 2.033 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: A 39 LEU cc_start: 0.9550 (tp) cc_final: 0.9148 (tp) REVERT: A 40 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8486 (tp40) REVERT: A 42 LYS cc_start: 0.9398 (tttt) cc_final: 0.9013 (pttt) REVERT: A 84 HIS cc_start: 0.9175 (m90) cc_final: 0.8750 (m90) REVERT: A 99 MET cc_start: 0.8513 (ttt) cc_final: 0.7627 (tmm) REVERT: A 113 GLU cc_start: 0.9343 (tt0) cc_final: 0.8836 (tm-30) REVERT: A 206 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9016 (mm110) REVERT: A 209 LYS cc_start: 0.8568 (mttt) cc_final: 0.8064 (ttmt) REVERT: A 215 MET cc_start: 0.9380 (mmm) cc_final: 0.8922 (mmm) REVERT: A 245 LYS cc_start: 0.8581 (mttt) cc_final: 0.8186 (mtpt) REVERT: A 255 MET cc_start: 0.9349 (tpp) cc_final: 0.9099 (tpp) REVERT: A 260 MET cc_start: 0.9637 (tpt) cc_final: 0.9341 (mmm) REVERT: A 282 GLU cc_start: 0.8926 (mp0) cc_final: 0.8689 (mm-30) REVERT: A 297 ILE cc_start: 0.9442 (mm) cc_final: 0.9192 (tp) REVERT: A 300 LYS cc_start: 0.9146 (mttt) cc_final: 0.8694 (mppt) REVERT: A 301 LYS cc_start: 0.9428 (tptt) cc_final: 0.8840 (tmtt) REVERT: A 306 GLN cc_start: 0.8887 (pt0) cc_final: 0.8610 (mp10) REVERT: A 343 PHE cc_start: 0.9635 (t80) cc_final: 0.9316 (t80) REVERT: A 347 CYS cc_start: 0.8954 (m) cc_final: 0.8450 (m) REVERT: A 399 ILE cc_start: 0.9239 (mt) cc_final: 0.9008 (mt) REVERT: A 403 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8851 (tp30) REVERT: A 410 MET cc_start: 0.9093 (tpt) cc_final: 0.8436 (tpp) REVERT: A 435 MET cc_start: 0.8837 (mmt) cc_final: 0.8554 (mmp) REVERT: A 440 MET cc_start: 0.8546 (tpt) cc_final: 0.8172 (tpp) REVERT: A 454 MET cc_start: 0.9235 (mtt) cc_final: 0.8862 (mmm) REVERT: A 463 CYS cc_start: 0.9412 (m) cc_final: 0.9124 (m) REVERT: A 483 GLN cc_start: 0.9622 (tt0) cc_final: 0.9215 (tp-100) REVERT: A 491 MET cc_start: 0.9131 (ttt) cc_final: 0.8805 (ttm) REVERT: A 494 CYS cc_start: 0.9144 (t) cc_final: 0.8908 (p) REVERT: A 497 MET cc_start: 0.9498 (ttp) cc_final: 0.8872 (ttp) REVERT: A 515 GLU cc_start: 0.9103 (tp30) cc_final: 0.8660 (tp30) REVERT: A 537 PHE cc_start: 0.9584 (t80) cc_final: 0.8596 (t80) REVERT: A 541 ILE cc_start: 0.8965 (pt) cc_final: 0.8268 (mm) REVERT: A 570 MET cc_start: 0.9489 (mmp) cc_final: 0.9140 (mmm) REVERT: A 577 MET cc_start: 0.9079 (mmt) cc_final: 0.8659 (mmm) REVERT: A 580 ASP cc_start: 0.8474 (m-30) cc_final: 0.7836 (m-30) REVERT: A 605 GLU cc_start: 0.9334 (tt0) cc_final: 0.9067 (tt0) REVERT: B 57 ASP cc_start: 0.9072 (m-30) cc_final: 0.8747 (m-30) REVERT: B 64 LEU cc_start: 0.9789 (tp) cc_final: 0.9526 (mt) REVERT: B 70 CYS cc_start: 0.8467 (p) cc_final: 0.7945 (p) REVERT: B 99 MET cc_start: 0.9271 (mtp) cc_final: 0.8807 (tpp) REVERT: B 110 MET cc_start: 0.9063 (mmm) cc_final: 0.8738 (mmm) REVERT: B 113 GLU cc_start: 0.9495 (tt0) cc_final: 0.9041 (tm-30) REVERT: B 118 GLN cc_start: 0.9431 (tt0) cc_final: 0.8996 (tp40) REVERT: B 123 ILE cc_start: 0.9569 (mt) cc_final: 0.9211 (mt) REVERT: B 128 GLN cc_start: 0.9097 (pt0) cc_final: 0.8257 (tm-30) REVERT: B 178 ILE cc_start: 0.9804 (mp) cc_final: 0.9580 (mp) REVERT: B 181 LEU cc_start: 0.9705 (tp) cc_final: 0.9421 (pp) REVERT: B 182 LEU cc_start: 0.9797 (mm) cc_final: 0.9516 (mm) REVERT: B 206 GLN cc_start: 0.9652 (mm-40) cc_final: 0.8945 (mm110) REVERT: B 209 LYS cc_start: 0.9174 (mttt) cc_final: 0.8617 (ttmt) REVERT: B 245 LYS cc_start: 0.9294 (mttt) cc_final: 0.8726 (ptpp) REVERT: B 250 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 260 MET cc_start: 0.9599 (mmm) cc_final: 0.9070 (mmm) REVERT: B 294 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 297 ILE cc_start: 0.9501 (pt) cc_final: 0.9275 (tp) REVERT: B 300 LYS cc_start: 0.8990 (mttt) cc_final: 0.8441 (mppt) REVERT: B 303 GLU cc_start: 0.9057 (tp30) cc_final: 0.8344 (tp30) REVERT: B 306 GLN cc_start: 0.8963 (pt0) cc_final: 0.8503 (pm20) REVERT: B 403 GLU cc_start: 0.9064 (tp30) cc_final: 0.8783 (tp30) REVERT: B 421 LEU cc_start: 0.9417 (tp) cc_final: 0.8923 (tp) REVERT: B 440 MET cc_start: 0.9380 (tpp) cc_final: 0.9164 (tpp) REVERT: B 454 MET cc_start: 0.9419 (mmt) cc_final: 0.8693 (tpp) REVERT: B 463 CYS cc_start: 0.9368 (m) cc_final: 0.9164 (m) REVERT: B 483 GLN cc_start: 0.9654 (tt0) cc_final: 0.9347 (tt0) REVERT: B 491 MET cc_start: 0.8956 (ttt) cc_final: 0.8567 (ttm) REVERT: B 494 CYS cc_start: 0.9055 (t) cc_final: 0.8829 (p) REVERT: B 497 MET cc_start: 0.9381 (ttp) cc_final: 0.8758 (ttp) REVERT: B 513 GLN cc_start: 0.9404 (tp-100) cc_final: 0.9022 (tp40) REVERT: B 518 GLU cc_start: 0.8846 (mp0) cc_final: 0.8612 (mp0) REVERT: B 528 MET cc_start: 0.8276 (mmp) cc_final: 0.7419 (mmm) REVERT: B 537 PHE cc_start: 0.9437 (t80) cc_final: 0.8202 (t80) REVERT: B 538 LEU cc_start: 0.9145 (mp) cc_final: 0.8930 (mp) REVERT: B 541 ILE cc_start: 0.9024 (pt) cc_final: 0.8744 (pt) REVERT: B 570 MET cc_start: 0.9460 (mmm) cc_final: 0.9257 (mmm) REVERT: B 574 LEU cc_start: 0.9774 (tp) cc_final: 0.9505 (tp) REVERT: C 35 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8933 (mt-10) REVERT: C 93 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8798 (pm20) REVERT: C 96 MET cc_start: 0.9273 (mmt) cc_final: 0.8890 (tmm) REVERT: C 110 MET cc_start: 0.9220 (mmm) cc_final: 0.8974 (mmm) REVERT: C 204 ILE cc_start: 0.9615 (mt) cc_final: 0.9375 (mt) REVERT: C 206 GLN cc_start: 0.9382 (mm-40) cc_final: 0.8789 (mm-40) REVERT: C 209 LYS cc_start: 0.8753 (mttt) cc_final: 0.8235 (mtpt) REVERT: C 215 MET cc_start: 0.9414 (mmp) cc_final: 0.9207 (mmm) REVERT: C 218 LEU cc_start: 0.9435 (tt) cc_final: 0.9206 (pp) REVERT: C 245 LYS cc_start: 0.8935 (mttt) cc_final: 0.8394 (ptpp) REVERT: C 246 LEU cc_start: 0.9697 (tp) cc_final: 0.9420 (tp) REVERT: C 250 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8542 (mm-30) REVERT: C 260 MET cc_start: 0.9680 (tpt) cc_final: 0.9390 (mmm) REVERT: C 297 ILE cc_start: 0.9523 (tp) cc_final: 0.9278 (tp) REVERT: C 300 LYS cc_start: 0.9135 (mttt) cc_final: 0.8653 (mppt) REVERT: C 301 LYS cc_start: 0.9474 (tptp) cc_final: 0.9053 (tmtt) REVERT: C 403 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8918 (tp30) REVERT: C 450 GLU cc_start: 0.9556 (pm20) cc_final: 0.9177 (pm20) REVERT: C 454 MET cc_start: 0.9219 (tpp) cc_final: 0.8578 (tpp) REVERT: C 458 LEU cc_start: 0.9844 (mm) cc_final: 0.9576 (mm) REVERT: C 497 MET cc_start: 0.8444 (tmm) cc_final: 0.7916 (tmm) REVERT: C 518 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8925 (tm-30) REVERT: C 570 MET cc_start: 0.9423 (mmp) cc_final: 0.9198 (mmm) REVERT: C 593 TRP cc_start: 0.9260 (t60) cc_final: 0.8924 (t60) REVERT: D 35 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8848 (mt-10) REVERT: D 93 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8908 (pm20) REVERT: D 96 MET cc_start: 0.9379 (mmp) cc_final: 0.8841 (mmm) REVERT: D 99 MET cc_start: 0.9045 (mtm) cc_final: 0.8637 (ptp) REVERT: D 113 GLU cc_start: 0.9568 (tt0) cc_final: 0.9297 (tm-30) REVERT: D 204 ILE cc_start: 0.9600 (mt) cc_final: 0.9371 (mt) REVERT: D 206 GLN cc_start: 0.9455 (mm-40) cc_final: 0.8896 (mm-40) REVERT: D 209 LYS cc_start: 0.8702 (mttt) cc_final: 0.8116 (ttmt) REVERT: D 215 MET cc_start: 0.9326 (mmp) cc_final: 0.8900 (mmm) REVERT: D 245 LYS cc_start: 0.8970 (mttt) cc_final: 0.8498 (ptpp) REVERT: D 246 LEU cc_start: 0.9689 (tp) cc_final: 0.9328 (tp) REVERT: D 250 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8505 (mm-30) REVERT: D 259 LEU cc_start: 0.9588 (mm) cc_final: 0.9373 (mm) REVERT: D 260 MET cc_start: 0.9664 (tpt) cc_final: 0.9342 (mmm) REVERT: D 300 LYS cc_start: 0.8965 (mttt) cc_final: 0.8524 (mppt) REVERT: D 301 LYS cc_start: 0.9232 (tptp) cc_final: 0.8728 (ttpt) REVERT: D 367 LEU cc_start: 0.9226 (tp) cc_final: 0.8760 (tp) REVERT: D 403 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8815 (tp30) REVERT: D 410 MET cc_start: 0.9264 (mmp) cc_final: 0.8970 (tpp) REVERT: D 454 MET cc_start: 0.9354 (mmt) cc_final: 0.8835 (mmt) REVERT: D 463 CYS cc_start: 0.9158 (m) cc_final: 0.8949 (m) REVERT: D 483 GLN cc_start: 0.9706 (tt0) cc_final: 0.9363 (tt0) REVERT: D 497 MET cc_start: 0.8769 (tmm) cc_final: 0.8525 (tmm) REVERT: D 518 GLU cc_start: 0.9045 (mp0) cc_final: 0.8801 (mp0) REVERT: D 536 LEU cc_start: 0.9762 (mt) cc_final: 0.9539 (mt) REVERT: D 570 MET cc_start: 0.9352 (mmp) cc_final: 0.9054 (mmm) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.2689 time to fit residues: 349.1750 Evaluate side-chains 701 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.1980 chunk 27 optimal weight: 0.0870 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 145 optimal weight: 0.0370 chunk 110 optimal weight: 8.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 582 HIS D 74 GLN D 267 GLN D 306 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20602 Z= 0.164 Angle : 0.708 7.819 27945 Z= 0.347 Chirality : 0.044 0.165 3138 Planarity : 0.004 0.057 3522 Dihedral : 5.298 49.546 2928 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2472 helix: -0.05 (0.14), residues: 1392 sheet: -3.49 (0.46), residues: 64 loop : -2.51 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 268 HIS 0.006 0.001 HIS D 84 PHE 0.020 0.001 PHE D 493 TYR 0.023 0.001 TYR C 161 ARG 0.008 0.000 ARG B 606 *********************** 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 828 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 828 time to evaluate : 2.222 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: A 39 LEU cc_start: 0.9575 (tp) cc_final: 0.9259 (tp) REVERT: A 42 LYS cc_start: 0.9321 (tttt) cc_final: 0.8972 (pttt) REVERT: A 99 MET cc_start: 0.8433 (ttt) cc_final: 0.7550 (tmm) REVERT: A 113 GLU cc_start: 0.9372 (tt0) cc_final: 0.8856 (tm-30) REVERT: A 206 GLN cc_start: 0.9473 (mm-40) cc_final: 0.8929 (mm-40) REVERT: A 209 LYS cc_start: 0.8606 (mttt) cc_final: 0.8096 (ttmt) REVERT: A 215 MET cc_start: 0.9403 (mmm) cc_final: 0.8944 (mmm) REVERT: A 245 LYS cc_start: 0.8546 (mttt) cc_final: 0.8184 (mtpt) REVERT: A 259 LEU cc_start: 0.9590 (mm) cc_final: 0.9380 (mm) REVERT: A 260 MET cc_start: 0.9631 (tpt) cc_final: 0.9327 (mmm) REVERT: A 297 ILE cc_start: 0.9405 (mm) cc_final: 0.9090 (tp) REVERT: A 300 LYS cc_start: 0.9229 (mttt) cc_final: 0.8756 (mppt) REVERT: A 301 LYS cc_start: 0.9323 (tptt) cc_final: 0.8669 (tmtt) REVERT: A 306 GLN cc_start: 0.8960 (pt0) cc_final: 0.8717 (mp10) REVERT: A 323 ARG cc_start: 0.8395 (ptp-110) cc_final: 0.7869 (ptm160) REVERT: A 343 PHE cc_start: 0.9613 (t80) cc_final: 0.9302 (t80) REVERT: A 347 CYS cc_start: 0.8904 (m) cc_final: 0.8374 (m) REVERT: A 403 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8866 (tp30) REVERT: A 410 MET cc_start: 0.9078 (tpt) cc_final: 0.8406 (tpp) REVERT: A 435 MET cc_start: 0.8903 (mmt) cc_final: 0.8604 (mmp) REVERT: A 440 MET cc_start: 0.8578 (tpt) cc_final: 0.8241 (tpp) REVERT: A 454 MET cc_start: 0.9227 (mtt) cc_final: 0.8872 (mmm) REVERT: A 463 CYS cc_start: 0.9427 (m) cc_final: 0.9221 (m) REVERT: A 483 GLN cc_start: 0.9593 (tt0) cc_final: 0.9176 (tp-100) REVERT: A 491 MET cc_start: 0.9127 (ttt) cc_final: 0.8809 (ttm) REVERT: A 494 CYS cc_start: 0.9134 (t) cc_final: 0.8892 (p) REVERT: A 497 MET cc_start: 0.9492 (ttp) cc_final: 0.8879 (ttp) REVERT: A 515 GLU cc_start: 0.9074 (tp30) cc_final: 0.8752 (tp30) REVERT: A 537 PHE cc_start: 0.9597 (t80) cc_final: 0.8631 (t80) REVERT: A 541 ILE cc_start: 0.8943 (pt) cc_final: 0.8237 (mm) REVERT: A 570 MET cc_start: 0.9503 (mmp) cc_final: 0.9181 (mmm) REVERT: A 577 MET cc_start: 0.9118 (mmt) cc_final: 0.8657 (mmm) REVERT: A 580 ASP cc_start: 0.8419 (m-30) cc_final: 0.7811 (m-30) REVERT: A 605 GLU cc_start: 0.9335 (tt0) cc_final: 0.9081 (tt0) REVERT: B 57 ASP cc_start: 0.9093 (m-30) cc_final: 0.8742 (m-30) REVERT: B 70 CYS cc_start: 0.8426 (p) cc_final: 0.7935 (p) REVERT: B 99 MET cc_start: 0.9325 (mtp) cc_final: 0.8861 (tpp) REVERT: B 110 MET cc_start: 0.9039 (mmm) cc_final: 0.8755 (mmm) REVERT: B 113 GLU cc_start: 0.9508 (tt0) cc_final: 0.9056 (tm-30) REVERT: B 118 GLN cc_start: 0.9437 (tt0) cc_final: 0.8999 (tp40) REVERT: B 123 ILE cc_start: 0.9560 (mt) cc_final: 0.9211 (mt) REVERT: B 128 GLN cc_start: 0.9090 (pt0) cc_final: 0.8161 (tm-30) REVERT: B 161 TYR cc_start: 0.8619 (t80) cc_final: 0.8302 (t80) REVERT: B 206 GLN cc_start: 0.9657 (mm-40) cc_final: 0.8947 (mm110) REVERT: B 209 LYS cc_start: 0.9157 (mttt) cc_final: 0.8766 (mtpt) REVERT: B 234 LEU cc_start: 0.8637 (mp) cc_final: 0.7515 (tp) REVERT: B 245 LYS cc_start: 0.9275 (mttt) cc_final: 0.8728 (ptpp) REVERT: B 250 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 260 MET cc_start: 0.9575 (mmm) cc_final: 0.9058 (mmm) REVERT: B 294 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 297 ILE cc_start: 0.9507 (pt) cc_final: 0.9265 (tp) REVERT: B 300 LYS cc_start: 0.8999 (mttt) cc_final: 0.8457 (mppt) REVERT: B 303 GLU cc_start: 0.9059 (tp30) cc_final: 0.8500 (tp30) REVERT: B 306 GLN cc_start: 0.8929 (pt0) cc_final: 0.8502 (pm20) REVERT: B 403 GLU cc_start: 0.9083 (tp30) cc_final: 0.8791 (tp30) REVERT: B 421 LEU cc_start: 0.9428 (tp) cc_final: 0.8945 (tp) REVERT: B 440 MET cc_start: 0.9398 (tpp) cc_final: 0.9189 (tpp) REVERT: B 454 MET cc_start: 0.9407 (mmt) cc_final: 0.8671 (tpp) REVERT: B 463 CYS cc_start: 0.9373 (m) cc_final: 0.9101 (m) REVERT: B 483 GLN cc_start: 0.9640 (tt0) cc_final: 0.9333 (tt0) REVERT: B 491 MET cc_start: 0.8935 (ttt) cc_final: 0.8519 (ttm) REVERT: B 494 CYS cc_start: 0.9047 (t) cc_final: 0.8816 (p) REVERT: B 497 MET cc_start: 0.9298 (ttp) cc_final: 0.8657 (ttp) REVERT: B 513 GLN cc_start: 0.9394 (tp-100) cc_final: 0.9049 (tp40) REVERT: B 528 MET cc_start: 0.8281 (mmp) cc_final: 0.7396 (mmm) REVERT: B 537 PHE cc_start: 0.9414 (t80) cc_final: 0.8188 (t80) REVERT: B 538 LEU cc_start: 0.9126 (mp) cc_final: 0.8905 (mp) REVERT: B 541 ILE cc_start: 0.9022 (pt) cc_final: 0.8736 (pt) REVERT: B 603 MET cc_start: 0.9634 (ttp) cc_final: 0.9169 (tmm) REVERT: B 604 LEU cc_start: 0.9826 (mm) cc_final: 0.9281 (mm) REVERT: C 34 ASP cc_start: 0.9439 (m-30) cc_final: 0.9197 (m-30) REVERT: C 35 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8887 (mp0) REVERT: C 93 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8788 (pm20) REVERT: C 96 MET cc_start: 0.9244 (mmt) cc_final: 0.8868 (tmm) REVERT: C 105 LEU cc_start: 0.9659 (tp) cc_final: 0.9437 (tp) REVERT: C 204 ILE cc_start: 0.9601 (mt) cc_final: 0.9362 (mt) REVERT: C 206 GLN cc_start: 0.9388 (mm-40) cc_final: 0.8811 (mm-40) REVERT: C 209 LYS cc_start: 0.8717 (mttt) cc_final: 0.8201 (mtpt) REVERT: C 218 LEU cc_start: 0.9422 (tt) cc_final: 0.9191 (pp) REVERT: C 245 LYS cc_start: 0.9130 (mttt) cc_final: 0.8509 (ptpp) REVERT: C 246 LEU cc_start: 0.9680 (tp) cc_final: 0.9395 (tp) REVERT: C 250 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8467 (mm-30) REVERT: C 260 MET cc_start: 0.9721 (tpt) cc_final: 0.9378 (mmm) REVERT: C 300 LYS cc_start: 0.9133 (mttt) cc_final: 0.8676 (mppt) REVERT: C 403 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8929 (tp30) REVERT: C 450 GLU cc_start: 0.9515 (pm20) cc_final: 0.8989 (pm20) REVERT: C 454 MET cc_start: 0.9254 (tpp) cc_final: 0.8581 (tpp) REVERT: C 458 LEU cc_start: 0.9833 (mm) cc_final: 0.9613 (mm) REVERT: C 463 CYS cc_start: 0.9276 (m) cc_final: 0.9026 (m) REVERT: C 483 GLN cc_start: 0.9638 (tt0) cc_final: 0.9381 (tt0) REVERT: C 497 MET cc_start: 0.8428 (tmm) cc_final: 0.7889 (tmm) REVERT: C 536 LEU cc_start: 0.9754 (mt) cc_final: 0.9532 (mt) REVERT: C 538 LEU cc_start: 0.9208 (mp) cc_final: 0.9001 (mp) REVERT: C 570 MET cc_start: 0.9415 (mmp) cc_final: 0.9206 (mmm) REVERT: C 589 ARG cc_start: 0.9281 (ptt90) cc_final: 0.9023 (ptm-80) REVERT: C 593 TRP cc_start: 0.9284 (t60) cc_final: 0.8955 (t60) REVERT: D 35 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8815 (mt-10) REVERT: D 93 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8869 (pm20) REVERT: D 96 MET cc_start: 0.9359 (mmp) cc_final: 0.8798 (mmm) REVERT: D 99 MET cc_start: 0.9019 (mtm) cc_final: 0.8635 (ptp) REVERT: D 113 GLU cc_start: 0.9578 (tt0) cc_final: 0.9282 (tm-30) REVERT: D 204 ILE cc_start: 0.9504 (mt) cc_final: 0.9209 (mt) REVERT: D 206 GLN cc_start: 0.9443 (mm-40) cc_final: 0.8878 (mm-40) REVERT: D 209 LYS cc_start: 0.8699 (mttt) cc_final: 0.8070 (ttmt) REVERT: D 215 MET cc_start: 0.9327 (mmp) cc_final: 0.8940 (mmt) REVERT: D 245 LYS cc_start: 0.9105 (mttt) cc_final: 0.8489 (ptpp) REVERT: D 246 LEU cc_start: 0.9586 (tp) cc_final: 0.9294 (tp) REVERT: D 250 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8656 (mm-30) REVERT: D 260 MET cc_start: 0.9661 (tpt) cc_final: 0.9351 (mmm) REVERT: D 267 GLN cc_start: 0.8178 (tm130) cc_final: 0.7909 (tm-30) REVERT: D 300 LYS cc_start: 0.8975 (mttt) cc_final: 0.8538 (mppt) REVERT: D 301 LYS cc_start: 0.9268 (tptp) cc_final: 0.8823 (ttpt) REVERT: D 323 ARG cc_start: 0.8527 (ptp-110) cc_final: 0.8085 (ptp-170) REVERT: D 343 PHE cc_start: 0.9569 (t80) cc_final: 0.9293 (t80) REVERT: D 403 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8801 (tp30) REVERT: D 410 MET cc_start: 0.9249 (mmp) cc_final: 0.8978 (tpp) REVERT: D 442 MET cc_start: 0.9675 (ttp) cc_final: 0.9341 (tmm) REVERT: D 454 MET cc_start: 0.9315 (mmt) cc_final: 0.8880 (mmm) REVERT: D 483 GLN cc_start: 0.9662 (tt0) cc_final: 0.9296 (tt0) REVERT: D 497 MET cc_start: 0.8792 (tmm) cc_final: 0.8496 (tmm) REVERT: D 515 GLU cc_start: 0.9091 (tp30) cc_final: 0.8538 (tp30) REVERT: D 518 GLU cc_start: 0.9079 (mp0) cc_final: 0.8836 (mp0) REVERT: D 536 LEU cc_start: 0.9749 (mt) cc_final: 0.9477 (mt) REVERT: D 570 MET cc_start: 0.9382 (mmp) cc_final: 0.9093 (mmm) REVERT: D 589 ARG cc_start: 0.9279 (ptt90) cc_final: 0.9069 (ptm-80) REVERT: D 631 LEU cc_start: 0.9519 (tt) cc_final: 0.9285 (tt) outliers start: 0 outliers final: 0 residues processed: 828 average time/residue: 0.2672 time to fit residues: 349.6007 Evaluate side-chains 697 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 162 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- 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 267 GLN A 464 ASN A 582 HIS B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 582 HIS D 37 ASN D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20602 Z= 0.175 Angle : 0.718 10.076 27945 Z= 0.353 Chirality : 0.045 0.170 3138 Planarity : 0.004 0.056 3522 Dihedral : 5.174 47.018 2928 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2472 helix: -0.09 (0.14), residues: 1420 sheet: -3.39 (0.47), residues: 64 loop : -2.57 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.008 0.001 HIS B 84 PHE 0.023 0.001 PHE B 162 TYR 0.013 0.001 TYR B 161 ARG 0.007 0.000 ARG B 606 *********************** 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 841 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 841 time to evaluate : 2.071 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: A 70 CYS cc_start: 0.8428 (t) cc_final: 0.7747 (t) REVERT: A 99 MET cc_start: 0.8449 (ttt) cc_final: 0.7543 (tmm) REVERT: A 113 GLU cc_start: 0.9390 (tt0) cc_final: 0.8877 (tm-30) REVERT: A 206 GLN cc_start: 0.9492 (mm-40) cc_final: 0.9135 (mm-40) REVERT: A 209 LYS cc_start: 0.8655 (mttt) cc_final: 0.8258 (ttmt) REVERT: A 215 MET cc_start: 0.9441 (mmm) cc_final: 0.9023 (mmm) REVERT: A 245 LYS cc_start: 0.8447 (mttt) cc_final: 0.8229 (mtpt) REVERT: A 259 LEU cc_start: 0.9597 (mm) cc_final: 0.9387 (mm) REVERT: A 260 MET cc_start: 0.9653 (tpt) cc_final: 0.9320 (mmm) REVERT: A 297 ILE cc_start: 0.9420 (mm) cc_final: 0.9118 (tp) REVERT: A 300 LYS cc_start: 0.9306 (mttt) cc_final: 0.8801 (mppt) REVERT: A 301 LYS cc_start: 0.9294 (tptt) cc_final: 0.8885 (tptp) REVERT: A 306 GLN cc_start: 0.9085 (pt0) cc_final: 0.8704 (mp10) REVERT: A 323 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8024 (ptp-110) REVERT: A 343 PHE cc_start: 0.9620 (t80) cc_final: 0.9302 (t80) REVERT: A 347 CYS cc_start: 0.8874 (m) cc_final: 0.8351 (m) REVERT: A 399 ILE cc_start: 0.9248 (mt) cc_final: 0.9029 (mt) REVERT: A 403 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8883 (tp30) REVERT: A 410 MET cc_start: 0.9088 (tpt) cc_final: 0.8346 (tpp) REVERT: A 435 MET cc_start: 0.8924 (mmt) cc_final: 0.8720 (mmp) REVERT: A 454 MET cc_start: 0.9278 (mtt) cc_final: 0.8890 (mmm) REVERT: A 463 CYS cc_start: 0.9402 (m) cc_final: 0.9141 (m) REVERT: A 483 GLN cc_start: 0.9605 (tt0) cc_final: 0.9237 (tt0) REVERT: A 491 MET cc_start: 0.9155 (ttt) cc_final: 0.8823 (ttm) REVERT: A 494 CYS cc_start: 0.9082 (t) cc_final: 0.8833 (p) REVERT: A 497 MET cc_start: 0.9501 (ttp) cc_final: 0.8916 (ttp) REVERT: A 515 GLU cc_start: 0.9055 (tp30) cc_final: 0.8771 (tp30) REVERT: A 526 TYR cc_start: 0.8799 (t80) cc_final: 0.8424 (t80) REVERT: A 537 PHE cc_start: 0.9602 (t80) cc_final: 0.8649 (t80) REVERT: A 541 ILE cc_start: 0.8964 (pt) cc_final: 0.8258 (mm) REVERT: A 570 MET cc_start: 0.9482 (mmp) cc_final: 0.9167 (mmm) REVERT: A 580 ASP cc_start: 0.8422 (m-30) cc_final: 0.8103 (m-30) REVERT: A 605 GLU cc_start: 0.9357 (tt0) cc_final: 0.9109 (tt0) REVERT: B 57 ASP cc_start: 0.9073 (m-30) cc_final: 0.8765 (m-30) REVERT: B 61 LEU cc_start: 0.9644 (mt) cc_final: 0.9376 (mt) REVERT: B 70 CYS cc_start: 0.8623 (p) cc_final: 0.8189 (p) REVERT: B 96 MET cc_start: 0.9656 (mmp) cc_final: 0.9414 (mmp) REVERT: B 99 MET cc_start: 0.9290 (mtp) cc_final: 0.8872 (tpp) REVERT: B 110 MET cc_start: 0.9070 (mmm) cc_final: 0.8798 (mmm) REVERT: B 113 GLU cc_start: 0.9502 (tt0) cc_final: 0.9033 (tm-30) REVERT: B 128 GLN cc_start: 0.9063 (pt0) cc_final: 0.8104 (tm-30) REVERT: B 132 LEU cc_start: 0.9850 (tp) cc_final: 0.9637 (tp) REVERT: B 136 LEU cc_start: 0.9527 (mt) cc_final: 0.9302 (mt) REVERT: B 206 GLN cc_start: 0.9628 (mm-40) cc_final: 0.8908 (mm110) REVERT: B 209 LYS cc_start: 0.9164 (mttt) cc_final: 0.8751 (mtpt) REVERT: B 245 LYS cc_start: 0.9268 (mttt) cc_final: 0.8701 (ptpp) REVERT: B 250 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8411 (mm-30) REVERT: B 255 MET cc_start: 0.9539 (tpp) cc_final: 0.9331 (tpp) REVERT: B 259 LEU cc_start: 0.9729 (mm) cc_final: 0.9489 (mm) REVERT: B 260 MET cc_start: 0.9579 (mmm) cc_final: 0.9049 (mmm) REVERT: B 294 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8729 (mt-10) REVERT: B 297 ILE cc_start: 0.9522 (pt) cc_final: 0.9303 (tp) REVERT: B 300 LYS cc_start: 0.9074 (mttt) cc_final: 0.8532 (mppt) REVERT: B 306 GLN cc_start: 0.8939 (pt0) cc_final: 0.8579 (mp10) REVERT: B 403 GLU cc_start: 0.9125 (tp30) cc_final: 0.8781 (tp30) REVERT: B 421 LEU cc_start: 0.9441 (tp) cc_final: 0.8966 (tp) REVERT: B 454 MET cc_start: 0.9411 (mmt) cc_final: 0.8690 (tpp) REVERT: B 463 CYS cc_start: 0.9326 (m) cc_final: 0.9123 (m) REVERT: B 483 GLN cc_start: 0.9627 (tt0) cc_final: 0.9328 (tt0) REVERT: B 491 MET cc_start: 0.8931 (ttt) cc_final: 0.8471 (ttm) REVERT: B 493 PHE cc_start: 0.9649 (t80) cc_final: 0.8713 (t80) REVERT: B 497 MET cc_start: 0.9324 (ttp) cc_final: 0.8604 (ttp) REVERT: B 513 GLN cc_start: 0.9404 (tp-100) cc_final: 0.9055 (tp40) REVERT: B 528 MET cc_start: 0.8256 (mmp) cc_final: 0.7405 (mmm) REVERT: B 537 PHE cc_start: 0.9389 (t80) cc_final: 0.8203 (t80) REVERT: B 541 ILE cc_start: 0.9038 (pt) cc_final: 0.8764 (pt) REVERT: C 34 ASP cc_start: 0.9454 (m-30) cc_final: 0.9234 (m-30) REVERT: C 35 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8928 (mp0) REVERT: C 93 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8796 (pm20) REVERT: C 96 MET cc_start: 0.9252 (mmt) cc_final: 0.8929 (tmm) REVERT: C 105 LEU cc_start: 0.9654 (tp) cc_final: 0.9418 (tp) REVERT: C 204 ILE cc_start: 0.9597 (mt) cc_final: 0.9357 (mt) REVERT: C 206 GLN cc_start: 0.9379 (mm-40) cc_final: 0.8773 (mm-40) REVERT: C 209 LYS cc_start: 0.8790 (mttt) cc_final: 0.8266 (ttmt) REVERT: C 215 MET cc_start: 0.9425 (mmp) cc_final: 0.8975 (mmm) REVERT: C 245 LYS cc_start: 0.9124 (mttt) cc_final: 0.8495 (ptpp) REVERT: C 246 LEU cc_start: 0.9684 (tp) cc_final: 0.9399 (tp) REVERT: C 250 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8536 (mm-30) REVERT: C 260 MET cc_start: 0.9730 (tpt) cc_final: 0.9368 (mmm) REVERT: C 300 LYS cc_start: 0.9139 (mttt) cc_final: 0.8646 (mppt) REVERT: C 301 LYS cc_start: 0.9413 (tptp) cc_final: 0.9007 (tmtt) REVERT: C 403 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8950 (tp30) REVERT: C 454 MET cc_start: 0.9313 (tpp) cc_final: 0.8659 (tpp) REVERT: C 458 LEU cc_start: 0.9848 (mm) cc_final: 0.9627 (mm) REVERT: C 463 CYS cc_start: 0.9259 (m) cc_final: 0.9003 (m) REVERT: C 483 GLN cc_start: 0.9623 (tt0) cc_final: 0.9313 (mm-40) REVERT: C 497 MET cc_start: 0.8420 (tmm) cc_final: 0.7873 (tmm) REVERT: C 538 LEU cc_start: 0.9194 (mp) cc_final: 0.8988 (mp) REVERT: C 570 MET cc_start: 0.9443 (mmp) cc_final: 0.9240 (mmm) REVERT: C 589 ARG cc_start: 0.9301 (ptt90) cc_final: 0.8994 (ptm-80) REVERT: D 35 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8824 (mt-10) REVERT: D 93 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8863 (pm20) REVERT: D 96 MET cc_start: 0.9353 (mmp) cc_final: 0.8799 (mmm) REVERT: D 99 MET cc_start: 0.9016 (mtm) cc_final: 0.8630 (ptp) REVERT: D 113 GLU cc_start: 0.9584 (tt0) cc_final: 0.9266 (tm-30) REVERT: D 204 ILE cc_start: 0.9520 (mt) cc_final: 0.9223 (mt) REVERT: D 206 GLN cc_start: 0.9454 (mm-40) cc_final: 0.8860 (mm-40) REVERT: D 209 LYS cc_start: 0.8761 (mttt) cc_final: 0.8248 (ttmt) REVERT: D 215 MET cc_start: 0.9369 (mmp) cc_final: 0.8980 (mmt) REVERT: D 245 LYS cc_start: 0.9080 (mttt) cc_final: 0.8454 (ptpp) REVERT: D 246 LEU cc_start: 0.9583 (tp) cc_final: 0.9272 (tp) REVERT: D 250 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8621 (mm-30) REVERT: D 260 MET cc_start: 0.9683 (tpt) cc_final: 0.9355 (mmm) REVERT: D 300 LYS cc_start: 0.9045 (mttt) cc_final: 0.8632 (mppt) REVERT: D 301 LYS cc_start: 0.9266 (tptp) cc_final: 0.8812 (ttpt) REVERT: D 323 ARG cc_start: 0.8599 (ptp-110) cc_final: 0.7930 (ptp-170) REVERT: D 343 PHE cc_start: 0.9571 (t80) cc_final: 0.9318 (t80) REVERT: D 403 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8804 (tp30) REVERT: D 410 MET cc_start: 0.9260 (mmp) cc_final: 0.9002 (tpp) REVERT: D 442 MET cc_start: 0.9673 (ttp) cc_final: 0.9364 (tmm) REVERT: D 454 MET cc_start: 0.9306 (mmt) cc_final: 0.8862 (mmm) REVERT: D 463 CYS cc_start: 0.9362 (m) cc_final: 0.9145 (m) REVERT: D 483 GLN cc_start: 0.9653 (tt0) cc_final: 0.9296 (tt0) REVERT: D 497 MET cc_start: 0.8801 (tmm) cc_final: 0.8365 (tmm) REVERT: D 518 GLU cc_start: 0.9094 (mp0) cc_final: 0.8849 (mp0) REVERT: D 570 MET cc_start: 0.9439 (mmp) cc_final: 0.9194 (mmm) REVERT: D 588 GLU cc_start: 0.9528 (pp20) cc_final: 0.9081 (pm20) REVERT: D 589 ARG cc_start: 0.9275 (ptt90) cc_final: 0.9032 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 841 average time/residue: 0.2653 time to fit residues: 354.9569 Evaluate side-chains 701 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 222 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 84 HIS A 267 GLN A 464 ASN A 582 HIS B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN D 217 ASN D 258 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 582 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20602 Z= 0.176 Angle : 0.736 11.221 27945 Z= 0.359 Chirality : 0.045 0.172 3138 Planarity : 0.004 0.057 3522 Dihedral : 5.032 41.730 2928 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2472 helix: 0.02 (0.14), residues: 1400 sheet: -3.36 (0.46), residues: 64 loop : -2.51 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 593 HIS 0.006 0.001 HIS B 84 PHE 0.024 0.001 PHE B 162 TYR 0.013 0.001 TYR A 324 ARG 0.006 0.000 ARG B 606 *********************** 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 787 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 787 time to evaluate : 2.174 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 34 ASP cc_start: 0.9525 (m-30) cc_final: 0.9283 (m-30) REVERT: A 39 LEU cc_start: 0.9615 (tp) cc_final: 0.9343 (tp) REVERT: A 42 LYS cc_start: 0.9270 (tttt) cc_final: 0.8910 (pttt) REVERT: A 70 CYS cc_start: 0.8421 (t) cc_final: 0.7748 (t) REVERT: A 99 MET cc_start: 0.8475 (ttt) cc_final: 0.7587 (tmm) REVERT: A 113 GLU cc_start: 0.9389 (tt0) cc_final: 0.8866 (tm-30) REVERT: A 184 GLU cc_start: 0.9514 (pt0) cc_final: 0.9107 (tm-30) REVERT: A 206 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8954 (mm-40) REVERT: A 209 LYS cc_start: 0.8704 (mttt) cc_final: 0.8235 (ttmt) REVERT: A 215 MET cc_start: 0.9439 (mmm) cc_final: 0.9008 (mmm) REVERT: A 245 LYS cc_start: 0.8482 (mttt) cc_final: 0.8028 (mtpp) REVERT: A 259 LEU cc_start: 0.9597 (mm) cc_final: 0.9370 (mm) REVERT: A 260 MET cc_start: 0.9658 (tpt) cc_final: 0.9325 (mmm) REVERT: A 297 ILE cc_start: 0.9421 (mm) cc_final: 0.9164 (tp) REVERT: A 300 LYS cc_start: 0.9316 (mttt) cc_final: 0.8811 (mppt) REVERT: A 301 LYS cc_start: 0.9283 (tptt) cc_final: 0.8943 (tmtt) REVERT: A 306 GLN cc_start: 0.9082 (pt0) cc_final: 0.8736 (mp10) REVERT: A 323 ARG cc_start: 0.8434 (ptp-110) cc_final: 0.8006 (tpt170) REVERT: A 343 PHE cc_start: 0.9617 (t80) cc_final: 0.9304 (t80) REVERT: A 347 CYS cc_start: 0.8868 (m) cc_final: 0.8366 (m) REVERT: A 399 ILE cc_start: 0.9256 (mt) cc_final: 0.9048 (mt) REVERT: A 403 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8886 (tp30) REVERT: A 410 MET cc_start: 0.9094 (tpt) cc_final: 0.8361 (tpp) REVERT: A 435 MET cc_start: 0.8936 (mmt) cc_final: 0.8729 (mmp) REVERT: A 440 MET cc_start: 0.9099 (tpp) cc_final: 0.8807 (tpp) REVERT: A 454 MET cc_start: 0.9296 (mtt) cc_final: 0.8899 (mmm) REVERT: A 463 CYS cc_start: 0.9445 (m) cc_final: 0.9188 (m) REVERT: A 483 GLN cc_start: 0.9594 (tt0) cc_final: 0.9190 (mm-40) REVERT: A 491 MET cc_start: 0.9150 (ttt) cc_final: 0.8820 (ttm) REVERT: A 494 CYS cc_start: 0.9059 (t) cc_final: 0.8801 (p) REVERT: A 497 MET cc_start: 0.9490 (ttp) cc_final: 0.8903 (ttp) REVERT: A 515 GLU cc_start: 0.9083 (tp30) cc_final: 0.8816 (tp30) REVERT: A 526 TYR cc_start: 0.8806 (t80) cc_final: 0.8469 (t80) REVERT: A 537 PHE cc_start: 0.9597 (t80) cc_final: 0.8629 (t80) REVERT: A 541 ILE cc_start: 0.8964 (pt) cc_final: 0.8248 (mm) REVERT: A 573 LEU cc_start: 0.9836 (tp) cc_final: 0.9632 (tp) REVERT: A 577 MET cc_start: 0.9512 (mmt) cc_final: 0.9280 (mmp) REVERT: A 605 GLU cc_start: 0.9333 (tt0) cc_final: 0.9088 (tt0) REVERT: A 631 LEU cc_start: 0.9496 (tt) cc_final: 0.9006 (tt) REVERT: B 57 ASP cc_start: 0.9067 (m-30) cc_final: 0.8638 (m-30) REVERT: B 70 CYS cc_start: 0.8575 (p) cc_final: 0.8148 (p) REVERT: B 96 MET cc_start: 0.9539 (mmp) cc_final: 0.9283 (mmm) REVERT: B 99 MET cc_start: 0.9129 (mtp) cc_final: 0.8868 (tpp) REVERT: B 110 MET cc_start: 0.9079 (mmm) cc_final: 0.8818 (mmm) REVERT: B 113 GLU cc_start: 0.9481 (tt0) cc_final: 0.8980 (tm-30) REVERT: B 118 GLN cc_start: 0.9488 (tt0) cc_final: 0.9157 (tm-30) REVERT: B 125 VAL cc_start: 0.9586 (t) cc_final: 0.9354 (p) REVERT: B 128 GLN cc_start: 0.8983 (pt0) cc_final: 0.7975 (tm-30) REVERT: B 206 GLN cc_start: 0.9617 (mm-40) cc_final: 0.8853 (mm110) REVERT: B 209 LYS cc_start: 0.9079 (mttt) cc_final: 0.8648 (mtmt) REVERT: B 245 LYS cc_start: 0.9248 (mttt) cc_final: 0.8686 (ptpp) REVERT: B 250 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 260 MET cc_start: 0.9569 (mmm) cc_final: 0.9068 (mmm) REVERT: B 294 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 297 ILE cc_start: 0.9531 (pt) cc_final: 0.9327 (tp) REVERT: B 300 LYS cc_start: 0.9062 (mttt) cc_final: 0.8524 (mppt) REVERT: B 306 GLN cc_start: 0.8813 (pt0) cc_final: 0.8480 (mp10) REVERT: B 421 LEU cc_start: 0.9462 (tp) cc_final: 0.9007 (tp) REVERT: B 454 MET cc_start: 0.9409 (mmt) cc_final: 0.8687 (tpp) REVERT: B 463 CYS cc_start: 0.9342 (m) cc_final: 0.9108 (m) REVERT: B 483 GLN cc_start: 0.9623 (tt0) cc_final: 0.9323 (tt0) REVERT: B 497 MET cc_start: 0.9161 (ttp) cc_final: 0.8681 (ttp) REVERT: B 513 GLN cc_start: 0.9400 (tp-100) cc_final: 0.9046 (tp40) REVERT: B 528 MET cc_start: 0.8221 (mmp) cc_final: 0.7333 (mmm) REVERT: B 537 PHE cc_start: 0.9417 (t80) cc_final: 0.8288 (t80) REVERT: B 541 ILE cc_start: 0.9067 (pt) cc_final: 0.8807 (pt) REVERT: C 35 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8972 (mt-10) REVERT: C 93 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8836 (pm20) REVERT: C 96 MET cc_start: 0.9248 (mmt) cc_final: 0.8975 (mmm) REVERT: C 105 LEU cc_start: 0.9656 (tp) cc_final: 0.9425 (tp) REVERT: C 204 ILE cc_start: 0.9598 (mt) cc_final: 0.9326 (mt) REVERT: C 209 LYS cc_start: 0.8817 (mttt) cc_final: 0.8246 (ttmt) REVERT: C 215 MET cc_start: 0.9400 (mmp) cc_final: 0.8971 (mmm) REVERT: C 245 LYS cc_start: 0.9125 (mttt) cc_final: 0.8587 (ptpp) REVERT: C 246 LEU cc_start: 0.9681 (tp) cc_final: 0.9370 (tp) REVERT: C 250 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8493 (mm-30) REVERT: C 259 LEU cc_start: 0.9630 (mm) cc_final: 0.9417 (mm) REVERT: C 260 MET cc_start: 0.9681 (tpt) cc_final: 0.9361 (mmm) REVERT: C 300 LYS cc_start: 0.9073 (mttt) cc_final: 0.8595 (mppt) REVERT: C 301 LYS cc_start: 0.9411 (tptp) cc_final: 0.9026 (tmtt) REVERT: C 403 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8972 (tp30) REVERT: C 454 MET cc_start: 0.9297 (tpp) cc_final: 0.8613 (tpp) REVERT: C 458 LEU cc_start: 0.9844 (mm) cc_final: 0.9627 (mm) REVERT: C 483 GLN cc_start: 0.9604 (tt0) cc_final: 0.9326 (tt0) REVERT: C 497 MET cc_start: 0.8369 (tmm) cc_final: 0.7842 (tmm) REVERT: C 518 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8977 (tm-30) REVERT: C 538 LEU cc_start: 0.9182 (mp) cc_final: 0.8964 (mp) REVERT: C 570 MET cc_start: 0.9450 (mmp) cc_final: 0.9242 (mmm) REVERT: C 578 MET cc_start: 0.9603 (mtm) cc_final: 0.9080 (mtt) REVERT: C 589 ARG cc_start: 0.9275 (ptt90) cc_final: 0.9029 (ptm-80) REVERT: C 593 TRP cc_start: 0.9174 (t60) cc_final: 0.8730 (t60) REVERT: D 34 ASP cc_start: 0.9456 (m-30) cc_final: 0.9185 (m-30) REVERT: D 35 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8770 (mt-10) REVERT: D 93 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8861 (pm20) REVERT: D 96 MET cc_start: 0.9366 (mmp) cc_final: 0.8807 (mmm) REVERT: D 99 MET cc_start: 0.8977 (mtm) cc_final: 0.8588 (ptp) REVERT: D 113 GLU cc_start: 0.9577 (tt0) cc_final: 0.9264 (tm-30) REVERT: D 204 ILE cc_start: 0.9526 (mt) cc_final: 0.9234 (mt) REVERT: D 206 GLN cc_start: 0.9443 (mm-40) cc_final: 0.8824 (mm-40) REVERT: D 209 LYS cc_start: 0.8776 (mttt) cc_final: 0.8150 (ttmt) REVERT: D 215 MET cc_start: 0.9364 (mmp) cc_final: 0.8989 (mmt) REVERT: D 245 LYS cc_start: 0.9066 (mttt) cc_final: 0.8439 (ptpp) REVERT: D 246 LEU cc_start: 0.9582 (tp) cc_final: 0.9258 (tp) REVERT: D 250 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8620 (mm-30) REVERT: D 259 LEU cc_start: 0.9607 (mm) cc_final: 0.9392 (mm) REVERT: D 260 MET cc_start: 0.9685 (tpt) cc_final: 0.9368 (mmm) REVERT: D 300 LYS cc_start: 0.9057 (mttt) cc_final: 0.8649 (mppt) REVERT: D 301 LYS cc_start: 0.9250 (tptp) cc_final: 0.8803 (ttpt) REVERT: D 323 ARG cc_start: 0.8589 (ptp-110) cc_final: 0.8021 (ptp-110) REVERT: D 343 PHE cc_start: 0.9570 (t80) cc_final: 0.9313 (t80) REVERT: D 403 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8801 (tp30) REVERT: D 410 MET cc_start: 0.9249 (mmp) cc_final: 0.9001 (tpp) REVERT: D 442 MET cc_start: 0.9663 (ttp) cc_final: 0.9447 (tmm) REVERT: D 454 MET cc_start: 0.9299 (mmt) cc_final: 0.8853 (mmm) REVERT: D 463 CYS cc_start: 0.9382 (m) cc_final: 0.9169 (m) REVERT: D 483 GLN cc_start: 0.9641 (tt0) cc_final: 0.9282 (tt0) REVERT: D 497 MET cc_start: 0.8790 (tmm) cc_final: 0.8268 (tmm) REVERT: D 515 GLU cc_start: 0.9073 (tp30) cc_final: 0.8474 (tp30) REVERT: D 518 GLU cc_start: 0.9113 (mp0) cc_final: 0.8870 (mp0) REVERT: D 570 MET cc_start: 0.9495 (mmp) cc_final: 0.9218 (mmm) outliers start: 0 outliers final: 0 residues processed: 787 average time/residue: 0.2725 time to fit residues: 339.4938 Evaluate side-chains 687 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 151 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 464 ASN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 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** D 464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20602 Z= 0.172 Angle : 0.736 13.177 27945 Z= 0.356 Chirality : 0.045 0.179 3138 Planarity : 0.004 0.057 3522 Dihedral : 4.971 37.537 2928 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2472 helix: 0.10 (0.14), residues: 1384 sheet: -3.38 (0.46), residues: 64 loop : -2.41 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 593 HIS 0.010 0.001 HIS D 582 PHE 0.020 0.001 PHE D 493 TYR 0.013 0.001 TYR B 216 ARG 0.006 0.000 ARG B 606 ********************** 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 834 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 834 time to evaluate : 2.412 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: A 70 CYS cc_start: 0.8413 (t) cc_final: 0.7762 (t) REVERT: A 99 MET cc_start: 0.8443 (ttt) cc_final: 0.7616 (tmm) REVERT: A 113 GLU cc_start: 0.9412 (tt0) cc_final: 0.8875 (tm-30) REVERT: A 181 LEU cc_start: 0.9791 (mt) cc_final: 0.9543 (tp) REVERT: A 206 GLN cc_start: 0.9474 (mm-40) cc_final: 0.8932 (mm-40) REVERT: A 209 LYS cc_start: 0.8733 (mttt) cc_final: 0.8304 (ttmt) REVERT: A 215 MET cc_start: 0.9442 (mmm) cc_final: 0.9009 (mmm) REVERT: A 245 LYS cc_start: 0.8714 (mttt) cc_final: 0.8294 (mtpp) REVERT: A 260 MET cc_start: 0.9651 (tpt) cc_final: 0.9329 (mmm) REVERT: A 297 ILE cc_start: 0.9429 (mm) cc_final: 0.9174 (tp) REVERT: A 300 LYS cc_start: 0.9378 (mttt) cc_final: 0.8886 (mppt) REVERT: A 301 LYS cc_start: 0.9271 (tptt) cc_final: 0.8828 (tptp) REVERT: A 306 GLN cc_start: 0.9061 (pt0) cc_final: 0.8749 (mp10) REVERT: A 343 PHE cc_start: 0.9629 (t80) cc_final: 0.9327 (t80) REVERT: A 347 CYS cc_start: 0.8851 (m) cc_final: 0.8363 (m) REVERT: A 403 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8887 (tp30) REVERT: A 410 MET cc_start: 0.9104 (tpt) cc_final: 0.8389 (tpp) REVERT: A 435 MET cc_start: 0.8928 (mmt) cc_final: 0.8677 (mmp) REVERT: A 440 MET cc_start: 0.9086 (tpp) cc_final: 0.8790 (tpp) REVERT: A 454 MET cc_start: 0.9298 (mtt) cc_final: 0.8901 (mmm) REVERT: A 463 CYS cc_start: 0.9479 (m) cc_final: 0.9217 (m) REVERT: A 491 MET cc_start: 0.9146 (ttt) cc_final: 0.8800 (ttm) REVERT: A 493 PHE cc_start: 0.9801 (t80) cc_final: 0.9305 (t80) REVERT: A 494 CYS cc_start: 0.9056 (t) cc_final: 0.8813 (p) REVERT: A 497 MET cc_start: 0.9478 (ttp) cc_final: 0.8873 (ttp) REVERT: A 515 GLU cc_start: 0.9070 (tp30) cc_final: 0.8792 (tp30) REVERT: A 526 TYR cc_start: 0.8804 (t80) cc_final: 0.8482 (t80) REVERT: A 537 PHE cc_start: 0.9611 (t80) cc_final: 0.8614 (t80) REVERT: A 541 ILE cc_start: 0.8975 (pt) cc_final: 0.8263 (mm) REVERT: A 570 MET cc_start: 0.9521 (mmm) cc_final: 0.9250 (mmm) REVERT: A 605 GLU cc_start: 0.9332 (tt0) cc_final: 0.9123 (tt0) REVERT: A 631 LEU cc_start: 0.9523 (tt) cc_final: 0.9199 (tt) REVERT: B 57 ASP cc_start: 0.9075 (m-30) cc_final: 0.8637 (m-30) REVERT: B 70 CYS cc_start: 0.8522 (p) cc_final: 0.8103 (p) REVERT: B 96 MET cc_start: 0.9578 (mmp) cc_final: 0.9190 (mmm) REVERT: B 99 MET cc_start: 0.9132 (mtp) cc_final: 0.8855 (tpp) REVERT: B 110 MET cc_start: 0.9066 (mmm) cc_final: 0.8808 (mmm) REVERT: B 113 GLU cc_start: 0.9468 (tt0) cc_final: 0.8955 (tm-30) REVERT: B 128 GLN cc_start: 0.9036 (pt0) cc_final: 0.8024 (tm-30) REVERT: B 206 GLN cc_start: 0.9621 (mm-40) cc_final: 0.8850 (mm110) REVERT: B 209 LYS cc_start: 0.9100 (mttt) cc_final: 0.8676 (mtmt) REVERT: B 245 LYS cc_start: 0.9266 (mttt) cc_final: 0.8698 (ptpp) REVERT: B 250 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8355 (mm-30) REVERT: B 260 MET cc_start: 0.9562 (mmm) cc_final: 0.9133 (mmm) REVERT: B 294 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8739 (mt-10) REVERT: B 300 LYS cc_start: 0.9102 (mttt) cc_final: 0.8554 (mppt) REVERT: B 329 PHE cc_start: 0.9404 (t80) cc_final: 0.9188 (t80) REVERT: B 421 LEU cc_start: 0.9463 (tp) cc_final: 0.9016 (tp) REVERT: B 454 MET cc_start: 0.9427 (mmt) cc_final: 0.8718 (tpp) REVERT: B 463 CYS cc_start: 0.9333 (m) cc_final: 0.9111 (m) REVERT: B 483 GLN cc_start: 0.9604 (tt0) cc_final: 0.9330 (tt0) REVERT: B 497 MET cc_start: 0.9162 (ttp) cc_final: 0.8703 (ttp) REVERT: B 513 GLN cc_start: 0.9387 (tp-100) cc_final: 0.9033 (tp40) REVERT: B 528 MET cc_start: 0.8205 (mmp) cc_final: 0.7310 (mmm) REVERT: B 537 PHE cc_start: 0.9418 (t80) cc_final: 0.8312 (t80) REVERT: B 541 ILE cc_start: 0.9075 (pt) cc_final: 0.8812 (pt) REVERT: C 35 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8938 (mt-10) REVERT: C 93 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8820 (pm20) REVERT: C 96 MET cc_start: 0.9242 (mmt) cc_final: 0.8982 (mmm) REVERT: C 137 LEU cc_start: 0.9605 (mt) cc_final: 0.9362 (pp) REVERT: C 200 LEU cc_start: 0.9446 (mm) cc_final: 0.9125 (mt) REVERT: C 204 ILE cc_start: 0.9577 (mt) cc_final: 0.9320 (mt) REVERT: C 209 LYS cc_start: 0.8841 (mttt) cc_final: 0.8200 (ttmt) REVERT: C 245 LYS cc_start: 0.9113 (mttt) cc_final: 0.8588 (ptpp) REVERT: C 246 LEU cc_start: 0.9672 (tp) cc_final: 0.9361 (tp) REVERT: C 250 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8473 (mm-30) REVERT: C 260 MET cc_start: 0.9654 (tpt) cc_final: 0.9358 (mmm) REVERT: C 300 LYS cc_start: 0.9149 (mttt) cc_final: 0.8648 (mppt) REVERT: C 301 LYS cc_start: 0.9363 (tptp) cc_final: 0.8964 (tmtt) REVERT: C 367 LEU cc_start: 0.9570 (tp) cc_final: 0.9245 (tp) REVERT: C 403 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8997 (tp30) REVERT: C 454 MET cc_start: 0.9325 (tpp) cc_final: 0.9119 (mmm) REVERT: C 463 CYS cc_start: 0.9201 (m) cc_final: 0.8957 (m) REVERT: C 466 MET cc_start: 0.9460 (mmp) cc_final: 0.9209 (mmp) REVERT: C 483 GLN cc_start: 0.9598 (tt0) cc_final: 0.9184 (mm-40) REVERT: C 497 MET cc_start: 0.8374 (tmm) cc_final: 0.7849 (tmm) REVERT: C 538 LEU cc_start: 0.9182 (mp) cc_final: 0.8956 (mp) REVERT: C 570 MET cc_start: 0.9454 (mmp) cc_final: 0.9231 (mmm) REVERT: C 578 MET cc_start: 0.9611 (mtm) cc_final: 0.9025 (mtm) REVERT: C 589 ARG cc_start: 0.9266 (ptt90) cc_final: 0.9035 (ptm-80) REVERT: C 593 TRP cc_start: 0.9200 (t60) cc_final: 0.8810 (t60) REVERT: C 631 LEU cc_start: 0.9509 (tt) cc_final: 0.9248 (tt) REVERT: D 35 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8775 (mt-10) REVERT: D 93 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8806 (pm20) REVERT: D 96 MET cc_start: 0.9363 (mmp) cc_final: 0.8828 (mmm) REVERT: D 99 MET cc_start: 0.8996 (mtm) cc_final: 0.8646 (ptp) REVERT: D 113 GLU cc_start: 0.9573 (tt0) cc_final: 0.9262 (tm-30) REVERT: D 204 ILE cc_start: 0.9513 (mt) cc_final: 0.9237 (mt) REVERT: D 206 GLN cc_start: 0.9408 (mm-40) cc_final: 0.8776 (mm-40) REVERT: D 209 LYS cc_start: 0.8811 (mttt) cc_final: 0.8222 (ttmt) REVERT: D 215 MET cc_start: 0.9357 (mmp) cc_final: 0.8990 (mmt) REVERT: D 245 LYS cc_start: 0.9019 (mttt) cc_final: 0.8396 (ptpp) REVERT: D 246 LEU cc_start: 0.9588 (tp) cc_final: 0.9336 (tp) REVERT: D 260 MET cc_start: 0.9686 (tpt) cc_final: 0.9376 (mmm) REVERT: D 300 LYS cc_start: 0.9123 (mttt) cc_final: 0.8614 (mppt) REVERT: D 303 GLU cc_start: 0.8689 (pp20) cc_final: 0.8050 (pp20) REVERT: D 323 ARG cc_start: 0.8555 (ptp-110) cc_final: 0.8020 (ptp-110) REVERT: D 343 PHE cc_start: 0.9574 (t80) cc_final: 0.9320 (t80) REVERT: D 403 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8804 (tp30) REVERT: D 410 MET cc_start: 0.9235 (mmp) cc_final: 0.9007 (tpp) REVERT: D 442 MET cc_start: 0.9659 (ttp) cc_final: 0.9350 (ppp) REVERT: D 454 MET cc_start: 0.9288 (mmt) cc_final: 0.8857 (mmm) REVERT: D 483 GLN cc_start: 0.9629 (tt0) cc_final: 0.9274 (tt0) REVERT: D 497 MET cc_start: 0.8734 (tmm) cc_final: 0.8190 (tmm) REVERT: D 515 GLU cc_start: 0.9082 (tp30) cc_final: 0.8316 (tp30) REVERT: D 526 TYR cc_start: 0.8979 (t80) cc_final: 0.8774 (t80) REVERT: D 570 MET cc_start: 0.9468 (mmp) cc_final: 0.9187 (mmm) outliers start: 0 outliers final: 0 residues processed: 834 average time/residue: 0.2668 time to fit residues: 355.1567 Evaluate side-chains 692 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 267 GLN A 464 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 572 ASN C 582 HIS D 74 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.059354 restraints weight = 60913.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062286 restraints weight = 34000.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064509 restraints weight = 22623.342| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20602 Z= 0.175 Angle : 0.745 10.313 27945 Z= 0.360 Chirality : 0.045 0.189 3138 Planarity : 0.004 0.054 3522 Dihedral : 4.878 34.193 2928 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2472 helix: 0.13 (0.14), residues: 1384 sheet: -3.24 (0.47), residues: 64 loop : -2.37 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 593 HIS 0.008 0.001 HIS D 582 PHE 0.017 0.001 PHE B 162 TYR 0.017 0.001 TYR A 324 ARG 0.006 0.000 ARG B 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6028.35 seconds wall clock time: 106 minutes 28.16 seconds (6388.16 seconds total)