Starting phenix.real_space_refine on Wed Nov 19 05:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvp_20496/11_2025/6pvp_20496.map" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 1 4.78 5 C 13864 2.51 5 N 3548 2.21 5 O 3888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21425 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5356 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 640} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.37, per 1000 atoms: 0.25 Number of scatterers: 21425 At special positions: 0 Unit cell: (144.16, 143.1, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 1 11.00 O 3888 8.00 N 3548 7.00 C 13864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 841.5 milliseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 4 sheets defined 62.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 4.199A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.028A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 4.232A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.520A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.825A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.616A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.689A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.717A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.507A pdb=" N LYS A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.549A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 563 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 607 removed outlier: 4.106A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER A 620 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.801A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 696 " --> pdb=" O TRP A 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.200A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.029A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.520A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.825A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.565A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.615A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.716A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 514 through 520 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.548A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 563 Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER B 620 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.653A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.800A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 696 " --> pdb=" O TRP B 692 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 4.201A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.030A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.519A pdb=" N LEU C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.826A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.616A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.716A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 514 through 520 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.549A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 563 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.803A pdb=" N SER C 620 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.801A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 696 " --> pdb=" O TRP C 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 4.200A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.029A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.519A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.826A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.615A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 334 " --> pdb=" O TRP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 363 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.717A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 506 No H-bonds generated for 'chain 'D' and resid 504 through 506' Processing helix chain 'D' and resid 514 through 520 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.550A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 563 Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER D 620 " --> pdb=" O LYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.800A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 696 " --> pdb=" O TRP D 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER A 386 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER B 386 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER C 386 " --> pdb=" O ASN C 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER D 386 " --> pdb=" O ASN D 735 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.34 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: 6750 1.34 - 1.46: 4704 1.46 - 1.58: 10226 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21884 Sorted by residual: bond pdb=" CA GLU A 687 " pdb=" CB GLU A 687 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.33e-02 5.65e+03 5.72e+00 bond pdb=" CA GLU D 687 " pdb=" CB GLU D 687 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.33e-02 5.65e+03 5.43e+00 bond pdb=" CA GLU B 687 " pdb=" CB GLU B 687 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.33e-02 5.65e+03 5.43e+00 bond pdb=" CA GLU C 687 " pdb=" CB GLU C 687 " ideal model delta sigma weight residual 1.524 1.493 0.030 1.33e-02 5.65e+03 5.21e+00 bond pdb=" C SER C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.80e+00 ... (remaining 21879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 28031 2.38 - 4.76: 1265 4.76 - 7.14: 255 7.14 - 9.52: 57 9.52 - 11.90: 24 Bond angle restraints: 29632 Sorted by residual: angle pdb=" C GLU D 418 " pdb=" N MET D 419 " pdb=" CA MET D 419 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" C GLN B 112 " pdb=" N ARG B 113 " pdb=" CA ARG B 113 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C GLU A 418 " pdb=" N MET A 419 " pdb=" CA MET A 419 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C GLU C 418 " pdb=" N MET C 419 " pdb=" CA MET C 419 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C GLU B 418 " pdb=" N MET B 419 " pdb=" CA MET B 419 " ideal model delta sigma weight residual 121.54 133.39 -11.85 1.91e+00 2.74e-01 3.85e+01 ... (remaining 29627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 11959 15.54 - 31.08: 897 31.08 - 46.62: 236 46.62 - 62.17: 44 62.17 - 77.71: 20 Dihedral angle restraints: 13156 sinusoidal: 5344 harmonic: 7812 Sorted by residual: dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N THR D 94 " pdb=" CA THR D 94 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA VAL A 93 " pdb=" C VAL A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA VAL C 93 " pdb=" C VAL C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta harmonic sigma weight residual 180.00 130.07 49.93 0 5.00e+00 4.00e-02 9.97e+01 ... (remaining 13153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1980 0.046 - 0.091: 1040 0.091 - 0.137: 273 0.137 - 0.183: 68 0.183 - 0.228: 23 Chirality restraints: 3384 Sorted by residual: chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL B 154 " pdb=" CA VAL B 154 " pdb=" CG1 VAL B 154 " pdb=" CG2 VAL B 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3381 not shown) Planarity restraints: 3724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 648 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C SER D 648 " -0.037 2.00e-02 2.50e+03 pdb=" O SER D 648 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 649 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 648 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C SER A 648 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 648 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 649 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 648 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C SER C 648 " 0.036 2.00e-02 2.50e+03 pdb=" O SER C 648 " -0.013 2.00e-02 2.50e+03 pdb=" N THR C 649 " -0.012 2.00e-02 2.50e+03 ... (remaining 3721 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4094 2.76 - 3.29: 21356 3.29 - 3.83: 35071 3.83 - 4.36: 39942 4.36 - 4.90: 63049 Nonbonded interactions: 163512 Sorted by model distance: nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR C 594 " pdb=" OG1 THR C 636 " model vdw 2.282 3.040 ... (remaining 163507 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' and resid 85 through 745) selection = chain 'B' 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.240 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.008 0.065 21884 Z= 0.384 Angle : 1.244 11.899 29632 Z= 0.659 Chirality : 0.058 0.228 3384 Planarity : 0.007 0.049 3724 Dihedral : 12.740 77.706 8076 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.63 % Favored : 84.22 % Rotamer: Outliers : 0.81 % Allowed : 10.59 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.94 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.24 (0.12), residues: 2636 helix: -3.00 (0.09), residues: 1380 sheet: -5.09 (0.40), residues: 48 loop : -4.00 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 416 TYR 0.018 0.003 TYR A 594 PHE 0.020 0.003 PHE D 728 TRP 0.027 0.004 TRP C 739 HIS 0.015 0.002 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00774 (21884) covalent geometry : angle 1.24407 (29632) hydrogen bonds : bond 0.32035 ( 916) hydrogen bonds : angle 9.38196 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 700 time to evaluate : 0.827 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 120 LYS cc_start: 0.9372 (tttt) cc_final: 0.9053 (ptpt) REVERT: A 129 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7805 (tm-30) REVERT: A 169 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7820 (pttt) REVERT: A 210 GLU cc_start: 0.8754 (tt0) cc_final: 0.8240 (tm-30) REVERT: A 321 TYR cc_start: 0.8419 (t80) cc_final: 0.7936 (t80) REVERT: A 388 SER cc_start: 0.8637 (m) cc_final: 0.8233 (p) REVERT: A 512 ASP cc_start: 0.6174 (m-30) cc_final: 0.5844 (t0) REVERT: A 526 PHE cc_start: 0.8083 (m-10) cc_final: 0.7692 (m-10) REVERT: A 550 CYS cc_start: 0.8657 (t) cc_final: 0.8442 (t) REVERT: A 572 MET cc_start: 0.9133 (mmt) cc_final: 0.8250 (mmm) REVERT: A 578 MET cc_start: 0.8624 (mtp) cc_final: 0.8218 (mtp) REVERT: A 632 LEU cc_start: 0.9374 (mt) cc_final: 0.9157 (mm) REVERT: A 702 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 210 GLU cc_start: 0.8707 (tt0) cc_final: 0.8485 (pt0) REVERT: B 448 TYR cc_start: 0.8713 (t80) cc_final: 0.7546 (t80) REVERT: B 493 TRP cc_start: 0.7082 (m100) cc_final: 0.6194 (m100) REVERT: B 550 CYS cc_start: 0.8742 (t) cc_final: 0.8473 (t) REVERT: B 572 MET cc_start: 0.9280 (mmt) cc_final: 0.8923 (mmm) REVERT: B 574 MET cc_start: 0.7762 (ppp) cc_final: 0.6470 (ppp) REVERT: B 578 MET cc_start: 0.8621 (mtp) cc_final: 0.7806 (mtt) REVERT: B 632 LEU cc_start: 0.9436 (mt) cc_final: 0.9139 (mm) REVERT: B 735 ASN cc_start: 0.7308 (m110) cc_final: 0.7101 (m110) REVERT: C 303 LEU cc_start: 0.9486 (mt) cc_final: 0.9202 (mp) REVERT: C 323 MET cc_start: 0.8450 (ttm) cc_final: 0.8183 (tpt) REVERT: C 388 SER cc_start: 0.8562 (m) cc_final: 0.8314 (p) REVERT: C 455 LEU cc_start: 0.9456 (tp) cc_final: 0.9255 (tp) REVERT: C 503 ILE cc_start: 0.8841 (mt) cc_final: 0.8600 (pt) REVERT: C 526 PHE cc_start: 0.7637 (m-10) cc_final: 0.7212 (m-80) REVERT: C 550 CYS cc_start: 0.8783 (t) cc_final: 0.8540 (t) REVERT: C 572 MET cc_start: 0.8917 (mmt) cc_final: 0.8629 (mmm) REVERT: C 574 MET cc_start: 0.7861 (ppp) cc_final: 0.6539 (ppp) REVERT: C 578 MET cc_start: 0.8796 (mtp) cc_final: 0.7699 (mtp) REVERT: C 632 LEU cc_start: 0.9439 (mt) cc_final: 0.9106 (mm) REVERT: D 120 LYS cc_start: 0.9344 (tttt) cc_final: 0.8949 (ptpt) REVERT: D 321 TYR cc_start: 0.8369 (t80) cc_final: 0.7964 (t80) REVERT: D 388 SER cc_start: 0.8629 (m) cc_final: 0.8359 (p) REVERT: D 440 MET cc_start: 0.8486 (mmt) cc_final: 0.8110 (mmp) REVERT: D 512 ASP cc_start: 0.5988 (m-30) cc_final: 0.5689 (t0) REVERT: D 526 PHE cc_start: 0.8080 (m-10) cc_final: 0.7731 (m-10) REVERT: D 572 MET cc_start: 0.9019 (mmt) cc_final: 0.8004 (mmm) REVERT: D 574 MET cc_start: 0.8027 (ppp) cc_final: 0.6699 (tmm) REVERT: D 578 MET cc_start: 0.8872 (mtp) cc_final: 0.8379 (mtt) REVERT: D 635 LEU cc_start: 0.9199 (mt) cc_final: 0.8522 (mt) REVERT: D 702 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 19 outliers final: 3 residues processed: 712 average time/residue: 0.1501 time to fit residues: 161.6895 Evaluate side-chains 421 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 418 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 255 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN C 99 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 255 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065786 restraints weight = 88036.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067301 restraints weight = 61466.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068384 restraints weight = 46740.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069033 restraints weight = 38402.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069655 restraints weight = 33463.547| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21884 Z= 0.204 Angle : 0.818 9.402 29632 Z= 0.431 Chirality : 0.042 0.153 3384 Planarity : 0.005 0.042 3724 Dihedral : 6.799 37.800 2864 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.81 % Favored : 85.89 % Rotamer: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.15), residues: 2636 helix: -0.94 (0.12), residues: 1436 sheet: -5.30 (0.32), residues: 64 loop : -3.40 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 567 TYR 0.016 0.002 TYR B 359 PHE 0.025 0.002 PHE D 124 TRP 0.018 0.002 TRP B 739 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00425 (21884) covalent geometry : angle 0.81751 (29632) hydrogen bonds : bond 0.06057 ( 916) hydrogen bonds : angle 5.04514 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 570 time to evaluate : 0.760 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 134 GLU cc_start: 0.8956 (pm20) cc_final: 0.8711 (pm20) REVERT: A 156 ASP cc_start: 0.9116 (m-30) cc_final: 0.8864 (m-30) REVERT: A 173 MET cc_start: 0.8888 (mtm) cc_final: 0.8309 (mmm) REVERT: A 321 TYR cc_start: 0.8946 (t80) cc_final: 0.8313 (t80) REVERT: A 418 GLU cc_start: 0.9129 (mp0) cc_final: 0.8794 (mp0) REVERT: A 423 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 448 TYR cc_start: 0.8663 (t80) cc_final: 0.8290 (t80) REVERT: A 464 ARG cc_start: 0.7354 (ttt180) cc_final: 0.6893 (ttt180) REVERT: A 493 TRP cc_start: 0.7349 (m100) cc_final: 0.6983 (m100) REVERT: A 512 ASP cc_start: 0.6400 (m-30) cc_final: 0.5799 (t0) REVERT: A 550 CYS cc_start: 0.9060 (t) cc_final: 0.8796 (t) REVERT: A 574 MET cc_start: 0.8415 (ppp) cc_final: 0.7177 (ppp) REVERT: A 578 MET cc_start: 0.8771 (mtp) cc_final: 0.8204 (mtt) REVERT: A 702 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 124 PHE cc_start: 0.8666 (m-10) cc_final: 0.8267 (m-80) REVERT: B 134 GLU cc_start: 0.8953 (pm20) cc_final: 0.8711 (pm20) REVERT: B 173 MET cc_start: 0.8745 (mtt) cc_final: 0.8464 (mmm) REVERT: B 234 LEU cc_start: 0.9431 (mm) cc_final: 0.9171 (mm) REVERT: B 271 CYS cc_start: 0.9466 (m) cc_final: 0.9031 (t) REVERT: B 423 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 448 TYR cc_start: 0.8819 (t80) cc_final: 0.7787 (t80) REVERT: B 451 TYR cc_start: 0.8927 (t80) cc_final: 0.8663 (t80) REVERT: B 484 LEU cc_start: 0.8718 (tp) cc_final: 0.8497 (tp) REVERT: B 493 TRP cc_start: 0.7571 (m100) cc_final: 0.6553 (m100) REVERT: B 529 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9010 (tm-30) REVERT: B 550 CYS cc_start: 0.8773 (t) cc_final: 0.8498 (t) REVERT: B 555 MET cc_start: 0.8871 (ttt) cc_final: 0.8575 (ttt) REVERT: B 574 MET cc_start: 0.7977 (ppp) cc_final: 0.7123 (ppp) REVERT: B 578 MET cc_start: 0.8979 (mtp) cc_final: 0.8547 (mtm) REVERT: B 687 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 158 LEU cc_start: 0.9474 (tt) cc_final: 0.9217 (pp) REVERT: C 173 MET cc_start: 0.8709 (mmp) cc_final: 0.7905 (mmp) REVERT: C 323 MET cc_start: 0.8884 (ttm) cc_final: 0.8581 (tpt) REVERT: C 388 SER cc_start: 0.8294 (m) cc_final: 0.7475 (p) REVERT: C 448 TYR cc_start: 0.8749 (t80) cc_final: 0.8303 (t80) REVERT: C 455 LEU cc_start: 0.9667 (tp) cc_final: 0.9366 (tp) REVERT: C 529 GLN cc_start: 0.9460 (tm-30) cc_final: 0.9077 (tm-30) REVERT: C 550 CYS cc_start: 0.8945 (t) cc_final: 0.8730 (t) REVERT: C 574 MET cc_start: 0.8059 (ppp) cc_final: 0.7095 (ppp) REVERT: C 578 MET cc_start: 0.8919 (mtp) cc_final: 0.8234 (mtm) REVERT: C 632 LEU cc_start: 0.9416 (mt) cc_final: 0.9104 (mm) REVERT: C 735 ASN cc_start: 0.7877 (m110) cc_final: 0.7586 (m110) REVERT: D 120 LYS cc_start: 0.9424 (tttt) cc_final: 0.9205 (ptpt) REVERT: D 131 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7452 (p) REVERT: D 134 GLU cc_start: 0.8915 (pm20) cc_final: 0.8498 (pm20) REVERT: D 156 ASP cc_start: 0.9097 (m-30) cc_final: 0.8834 (m-30) REVERT: D 173 MET cc_start: 0.8782 (mtm) cc_final: 0.8419 (mmm) REVERT: D 321 TYR cc_start: 0.8981 (t80) cc_final: 0.8403 (t80) REVERT: D 418 GLU cc_start: 0.8935 (mp0) cc_final: 0.8570 (mp0) REVERT: D 448 TYR cc_start: 0.8672 (t80) cc_final: 0.8292 (t80) REVERT: D 493 TRP cc_start: 0.7429 (m100) cc_final: 0.6296 (m100) REVERT: D 512 ASP cc_start: 0.6149 (m-30) cc_final: 0.5709 (t0) REVERT: D 550 CYS cc_start: 0.8798 (t) cc_final: 0.8561 (t) REVERT: D 574 MET cc_start: 0.8160 (ppp) cc_final: 0.7627 (ppp) REVERT: D 578 MET cc_start: 0.8751 (mtp) cc_final: 0.8066 (mtm) REVERT: D 631 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 702 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7907 (tm-30) outliers start: 4 outliers final: 0 residues processed: 574 average time/residue: 0.1326 time to fit residues: 119.8888 Evaluate side-chains 398 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 185 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063534 restraints weight = 89627.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065279 restraints weight = 60697.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066338 restraints weight = 45247.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067282 restraints weight = 36765.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067720 restraints weight = 31525.564| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 21884 Z= 0.227 Angle : 0.806 9.818 29632 Z= 0.416 Chirality : 0.043 0.210 3384 Planarity : 0.005 0.044 3724 Dihedral : 6.511 39.654 2864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.25 % Favored : 84.60 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.16), residues: 2636 helix: -0.31 (0.12), residues: 1504 sheet: -4.32 (0.46), residues: 48 loop : -3.55 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 464 TYR 0.020 0.002 TYR D 359 PHE 0.042 0.002 PHE C 526 TRP 0.023 0.002 TRP D 521 HIS 0.008 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00484 (21884) covalent geometry : angle 0.80582 (29632) hydrogen bonds : bond 0.04998 ( 916) hydrogen bonds : angle 4.81064 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.529 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 124 PHE cc_start: 0.8812 (m-80) cc_final: 0.8424 (m-80) REVERT: A 173 MET cc_start: 0.8693 (mtm) cc_final: 0.8370 (mmm) REVERT: A 301 HIS cc_start: 0.9194 (m170) cc_final: 0.8972 (m-70) REVERT: A 405 GLU cc_start: 0.8505 (tt0) cc_final: 0.8188 (mt-10) REVERT: A 418 GLU cc_start: 0.9090 (mp0) cc_final: 0.8642 (mp0) REVERT: A 423 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 448 TYR cc_start: 0.9195 (t80) cc_final: 0.8794 (t80) REVERT: A 493 TRP cc_start: 0.7445 (m100) cc_final: 0.6557 (m100) REVERT: A 512 ASP cc_start: 0.6532 (m-30) cc_final: 0.5930 (t0) REVERT: A 574 MET cc_start: 0.8127 (ppp) cc_final: 0.7464 (ppp) REVERT: A 578 MET cc_start: 0.8720 (mtp) cc_final: 0.8291 (mtm) REVERT: A 632 LEU cc_start: 0.9582 (mt) cc_final: 0.9365 (mt) REVERT: A 702 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 124 PHE cc_start: 0.8571 (m-10) cc_final: 0.8182 (m-80) REVERT: B 134 GLU cc_start: 0.8634 (pm20) cc_final: 0.8418 (pm20) REVERT: B 173 MET cc_start: 0.8715 (mtt) cc_final: 0.8411 (mmm) REVERT: B 210 GLU cc_start: 0.9184 (tt0) cc_final: 0.8877 (tt0) REVERT: B 423 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 448 TYR cc_start: 0.9013 (t80) cc_final: 0.8021 (t80) REVERT: B 493 TRP cc_start: 0.7907 (m100) cc_final: 0.7039 (m100) REVERT: B 529 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8921 (tm-30) REVERT: B 550 CYS cc_start: 0.8833 (t) cc_final: 0.8611 (t) REVERT: B 574 MET cc_start: 0.8075 (ppp) cc_final: 0.7288 (ppp) REVERT: B 578 MET cc_start: 0.8911 (mtp) cc_final: 0.8389 (mtm) REVERT: B 687 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 735 ASN cc_start: 0.6683 (m110) cc_final: 0.6199 (m110) REVERT: C 141 ASP cc_start: 0.9266 (t0) cc_final: 0.9038 (t0) REVERT: C 158 LEU cc_start: 0.9446 (tt) cc_final: 0.9222 (pp) REVERT: C 388 SER cc_start: 0.8177 (m) cc_final: 0.7361 (p) REVERT: C 448 TYR cc_start: 0.9121 (t80) cc_final: 0.8647 (t80) REVERT: C 455 LEU cc_start: 0.9687 (tp) cc_final: 0.9367 (tp) REVERT: C 574 MET cc_start: 0.8003 (ppp) cc_final: 0.7073 (ppp) REVERT: C 578 MET cc_start: 0.8924 (mtp) cc_final: 0.8477 (mtm) REVERT: C 632 LEU cc_start: 0.9510 (mt) cc_final: 0.9162 (mm) REVERT: C 687 GLU cc_start: 0.8818 (tt0) cc_final: 0.8577 (tm-30) REVERT: C 735 ASN cc_start: 0.7649 (m110) cc_final: 0.7400 (m110) REVERT: D 120 LYS cc_start: 0.9418 (tttt) cc_final: 0.9120 (ptpt) REVERT: D 124 PHE cc_start: 0.8746 (m-80) cc_final: 0.8544 (m-80) REVERT: D 173 MET cc_start: 0.8700 (mtm) cc_final: 0.8398 (mmm) REVERT: D 301 HIS cc_start: 0.9202 (m170) cc_final: 0.8970 (m-70) REVERT: D 418 GLU cc_start: 0.8947 (mp0) cc_final: 0.8520 (mp0) REVERT: D 448 TYR cc_start: 0.9164 (t80) cc_final: 0.8799 (t80) REVERT: D 455 LEU cc_start: 0.9498 (tp) cc_final: 0.9042 (tp) REVERT: D 512 ASP cc_start: 0.6535 (m-30) cc_final: 0.5949 (t0) REVERT: D 548 LEU cc_start: 0.9297 (tp) cc_final: 0.9044 (pt) REVERT: D 550 CYS cc_start: 0.8791 (t) cc_final: 0.8585 (t) REVERT: D 578 MET cc_start: 0.8737 (mtp) cc_final: 0.8511 (mtt) REVERT: D 702 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 730 LEU cc_start: 0.9216 (pt) cc_final: 0.9014 (pt) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.1295 time to fit residues: 102.8940 Evaluate side-chains 372 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 200 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 585 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062621 restraints weight = 87908.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064252 restraints weight = 59075.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.065427 restraints weight = 43859.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066168 restraints weight = 35230.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066839 restraints weight = 30390.966| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 21884 Z= 0.215 Angle : 0.785 10.663 29632 Z= 0.404 Chirality : 0.042 0.176 3384 Planarity : 0.005 0.106 3724 Dihedral : 6.327 39.213 2864 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.57 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.16), residues: 2636 helix: -0.01 (0.13), residues: 1492 sheet: -4.34 (0.49), residues: 56 loop : -3.48 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 464 TYR 0.020 0.002 TYR D 359 PHE 0.020 0.002 PHE A 590 TRP 0.023 0.002 TRP A 521 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00456 (21884) covalent geometry : angle 0.78489 (29632) hydrogen bonds : bond 0.04572 ( 916) hydrogen bonds : angle 4.70840 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.842 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 124 PHE cc_start: 0.8811 (m-80) cc_final: 0.8433 (m-80) REVERT: A 173 MET cc_start: 0.8724 (mtm) cc_final: 0.8456 (mmm) REVERT: A 301 HIS cc_start: 0.9199 (m170) cc_final: 0.8802 (m90) REVERT: A 323 MET cc_start: 0.8409 (tpt) cc_final: 0.7873 (tpt) REVERT: A 336 MET cc_start: 0.7858 (ttp) cc_final: 0.7548 (tmm) REVERT: A 405 GLU cc_start: 0.8475 (tt0) cc_final: 0.8201 (pt0) REVERT: A 418 GLU cc_start: 0.9004 (mp0) cc_final: 0.8577 (mp0) REVERT: A 423 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 448 TYR cc_start: 0.9247 (t80) cc_final: 0.8570 (t80) REVERT: A 493 TRP cc_start: 0.7366 (m100) cc_final: 0.6658 (m100) REVERT: A 512 ASP cc_start: 0.6570 (m-30) cc_final: 0.5943 (t0) REVERT: A 555 MET cc_start: 0.8936 (ttt) cc_final: 0.8664 (ttt) REVERT: A 572 MET cc_start: 0.9144 (mmm) cc_final: 0.8639 (mmm) REVERT: A 574 MET cc_start: 0.8237 (ppp) cc_final: 0.7176 (ppp) REVERT: A 578 MET cc_start: 0.8828 (mtp) cc_final: 0.8393 (mtt) REVERT: A 589 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8494 (mmtt) REVERT: A 632 LEU cc_start: 0.9514 (mt) cc_final: 0.9214 (mt) REVERT: A 702 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 133 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8826 (pm20) REVERT: B 141 ASP cc_start: 0.9055 (m-30) cc_final: 0.8737 (t0) REVERT: B 423 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 448 TYR cc_start: 0.9049 (t80) cc_final: 0.8470 (t80) REVERT: B 493 TRP cc_start: 0.7902 (m100) cc_final: 0.7070 (m100) REVERT: B 529 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9058 (tm-30) REVERT: B 550 CYS cc_start: 0.8878 (t) cc_final: 0.8596 (t) REVERT: B 574 MET cc_start: 0.8181 (ppp) cc_final: 0.7090 (ppp) REVERT: B 578 MET cc_start: 0.8929 (mtp) cc_final: 0.8195 (mtm) REVERT: B 672 MET cc_start: 0.8679 (mmm) cc_final: 0.8454 (tpt) REVERT: B 735 ASN cc_start: 0.6702 (m110) cc_final: 0.6110 (m110) REVERT: C 141 ASP cc_start: 0.9204 (t0) cc_final: 0.8970 (t0) REVERT: C 173 MET cc_start: 0.8540 (mmp) cc_final: 0.8238 (mmp) REVERT: C 301 HIS cc_start: 0.9309 (m170) cc_final: 0.9102 (m90) REVERT: C 388 SER cc_start: 0.8323 (m) cc_final: 0.7881 (m) REVERT: C 448 TYR cc_start: 0.9122 (t80) cc_final: 0.8536 (t80) REVERT: C 451 TYR cc_start: 0.8891 (t80) cc_final: 0.8673 (t80) REVERT: C 455 LEU cc_start: 0.9639 (tp) cc_final: 0.9171 (tp) REVERT: C 464 ARG cc_start: 0.6259 (mtt-85) cc_final: 0.5650 (ttt180) REVERT: C 529 GLN cc_start: 0.9371 (tp40) cc_final: 0.9030 (tp40) REVERT: C 550 CYS cc_start: 0.8707 (t) cc_final: 0.8422 (t) REVERT: C 574 MET cc_start: 0.8124 (ppp) cc_final: 0.7085 (ppp) REVERT: C 578 MET cc_start: 0.8907 (mtp) cc_final: 0.8519 (mtm) REVERT: C 632 LEU cc_start: 0.9533 (mt) cc_final: 0.9236 (mm) REVERT: D 173 MET cc_start: 0.8675 (mtm) cc_final: 0.8442 (mmm) REVERT: D 336 MET cc_start: 0.7822 (ttp) cc_final: 0.7604 (tmm) REVERT: D 418 GLU cc_start: 0.8895 (mp0) cc_final: 0.8536 (mp0) REVERT: D 451 TYR cc_start: 0.9054 (t80) cc_final: 0.8768 (t80) REVERT: D 493 TRP cc_start: 0.7850 (m100) cc_final: 0.6710 (m100) REVERT: D 512 ASP cc_start: 0.6543 (m-30) cc_final: 0.5886 (t0) REVERT: D 550 CYS cc_start: 0.8879 (t) cc_final: 0.8615 (t) REVERT: D 578 MET cc_start: 0.8795 (mtp) cc_final: 0.8486 (mtt) REVERT: D 589 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8517 (mmtt) REVERT: D 594 TYR cc_start: 0.7165 (t80) cc_final: 0.6946 (t80) REVERT: D 631 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 632 LEU cc_start: 0.9614 (mt) cc_final: 0.9150 (mt) REVERT: D 635 LEU cc_start: 0.9276 (mt) cc_final: 0.8919 (mt) REVERT: D 661 TYR cc_start: 0.8853 (t80) cc_final: 0.8263 (t80) REVERT: D 702 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8205 (tm-30) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.1283 time to fit residues: 102.2789 Evaluate side-chains 374 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 570 GLN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063082 restraints weight = 88381.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064699 restraints weight = 59183.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065917 restraints weight = 44128.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066558 restraints weight = 35595.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067270 restraints weight = 30944.968| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21884 Z= 0.177 Angle : 0.759 9.178 29632 Z= 0.389 Chirality : 0.042 0.181 3384 Planarity : 0.004 0.062 3724 Dihedral : 6.136 39.120 2864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.76 % Favored : 85.09 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2636 helix: 0.17 (0.13), residues: 1468 sheet: -3.90 (0.58), residues: 48 loop : -3.48 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 295 TYR 0.018 0.002 TYR B 359 PHE 0.027 0.001 PHE B 597 TRP 0.032 0.002 TRP C 742 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00382 (21884) covalent geometry : angle 0.75943 (29632) hydrogen bonds : bond 0.04354 ( 916) hydrogen bonds : angle 4.58811 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.865 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 173 MET cc_start: 0.8840 (mtm) cc_final: 0.8330 (mmt) REVERT: A 301 HIS cc_start: 0.9260 (m170) cc_final: 0.8720 (m90) REVERT: A 323 MET cc_start: 0.8520 (tpt) cc_final: 0.8158 (tpt) REVERT: A 405 GLU cc_start: 0.8521 (tt0) cc_final: 0.8265 (pt0) REVERT: A 418 GLU cc_start: 0.9030 (mp0) cc_final: 0.8660 (mp0) REVERT: A 423 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 448 TYR cc_start: 0.9294 (t80) cc_final: 0.8533 (t80) REVERT: A 455 LEU cc_start: 0.9523 (tp) cc_final: 0.9007 (tp) REVERT: A 493 TRP cc_start: 0.7532 (m100) cc_final: 0.6827 (m100) REVERT: A 512 ASP cc_start: 0.6737 (m-30) cc_final: 0.5905 (t0) REVERT: A 548 LEU cc_start: 0.9309 (pt) cc_final: 0.9081 (mm) REVERT: A 572 MET cc_start: 0.9103 (mmm) cc_final: 0.8654 (mmm) REVERT: A 574 MET cc_start: 0.8138 (ppp) cc_final: 0.7170 (ppp) REVERT: A 578 MET cc_start: 0.8906 (mtp) cc_final: 0.8384 (mtm) REVERT: A 589 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8478 (mmtt) REVERT: A 632 LEU cc_start: 0.9530 (mt) cc_final: 0.9241 (mt) REVERT: A 702 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 133 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8801 (pm20) REVERT: B 141 ASP cc_start: 0.9026 (m-30) cc_final: 0.8713 (t0) REVERT: B 210 GLU cc_start: 0.9233 (tt0) cc_final: 0.8919 (tt0) REVERT: B 388 SER cc_start: 0.8155 (m) cc_final: 0.7369 (p) REVERT: B 423 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 448 TYR cc_start: 0.9154 (t80) cc_final: 0.8569 (t80) REVERT: B 492 ILE cc_start: 0.9135 (tt) cc_final: 0.8865 (pt) REVERT: B 493 TRP cc_start: 0.7977 (m100) cc_final: 0.6973 (m100) REVERT: B 529 GLN cc_start: 0.9412 (tm-30) cc_final: 0.9202 (tm-30) REVERT: B 548 LEU cc_start: 0.9467 (pt) cc_final: 0.9125 (mp) REVERT: B 557 LEU cc_start: 0.8476 (mm) cc_final: 0.8103 (tp) REVERT: B 574 MET cc_start: 0.8025 (ppp) cc_final: 0.6926 (ppp) REVERT: B 578 MET cc_start: 0.8874 (mtp) cc_final: 0.8118 (mtm) REVERT: B 594 TYR cc_start: 0.7946 (t80) cc_final: 0.7733 (t80) REVERT: B 601 PHE cc_start: 0.8824 (m-80) cc_final: 0.7873 (m-80) REVERT: B 735 ASN cc_start: 0.6934 (m110) cc_final: 0.6381 (m-40) REVERT: C 141 ASP cc_start: 0.9227 (t0) cc_final: 0.8977 (t0) REVERT: C 388 SER cc_start: 0.8145 (m) cc_final: 0.7398 (m) REVERT: C 418 GLU cc_start: 0.9221 (mp0) cc_final: 0.8878 (mp0) REVERT: C 451 TYR cc_start: 0.8985 (t80) cc_final: 0.8774 (t80) REVERT: C 488 MET cc_start: 0.8628 (ppp) cc_final: 0.8362 (ppp) REVERT: C 492 ILE cc_start: 0.8997 (tt) cc_final: 0.8785 (tt) REVERT: C 493 TRP cc_start: 0.7722 (m100) cc_final: 0.6679 (m100) REVERT: C 529 GLN cc_start: 0.9545 (tp40) cc_final: 0.8905 (tp40) REVERT: C 557 LEU cc_start: 0.8904 (mm) cc_final: 0.8595 (tp) REVERT: C 574 MET cc_start: 0.8031 (ppp) cc_final: 0.7533 (ppp) REVERT: C 594 TYR cc_start: 0.7971 (t80) cc_final: 0.7733 (t80) REVERT: C 632 LEU cc_start: 0.9543 (mt) cc_final: 0.9258 (mm) REVERT: C 730 LEU cc_start: 0.9027 (pt) cc_final: 0.8824 (pt) REVERT: D 173 MET cc_start: 0.8839 (mtm) cc_final: 0.8365 (mmm) REVERT: D 301 HIS cc_start: 0.9237 (m170) cc_final: 0.8722 (m90) REVERT: D 323 MET cc_start: 0.8705 (tpt) cc_final: 0.8171 (tpt) REVERT: D 418 GLU cc_start: 0.8862 (mp0) cc_final: 0.8506 (mp0) REVERT: D 448 TYR cc_start: 0.9273 (t80) cc_final: 0.8462 (t80) REVERT: D 493 TRP cc_start: 0.7921 (m100) cc_final: 0.6799 (m100) REVERT: D 512 ASP cc_start: 0.6635 (m-30) cc_final: 0.5935 (t0) REVERT: D 548 LEU cc_start: 0.9409 (pt) cc_final: 0.9147 (mm) REVERT: D 578 MET cc_start: 0.8817 (mtp) cc_final: 0.8342 (mtm) REVERT: D 631 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 632 LEU cc_start: 0.9656 (mt) cc_final: 0.9167 (mt) REVERT: D 635 LEU cc_start: 0.9210 (mt) cc_final: 0.8996 (mt) REVERT: D 655 LEU cc_start: 0.9457 (mt) cc_final: 0.9235 (pp) REVERT: D 661 TYR cc_start: 0.9084 (t80) cc_final: 0.8433 (t80) REVERT: D 702 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 730 LEU cc_start: 0.9180 (pt) cc_final: 0.8979 (pt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.1259 time to fit residues: 103.9079 Evaluate side-chains 382 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 150 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN A 561 ASN A 585 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 585 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063474 restraints weight = 87806.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065057 restraints weight = 59349.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.066215 restraints weight = 44444.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067111 restraints weight = 36010.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067463 restraints weight = 30771.377| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21884 Z= 0.160 Angle : 0.749 8.926 29632 Z= 0.380 Chirality : 0.041 0.182 3384 Planarity : 0.004 0.063 3724 Dihedral : 5.979 37.129 2864 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.30 % Favored : 85.55 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2636 helix: 0.27 (0.13), residues: 1468 sheet: -3.72 (0.61), residues: 48 loop : -3.44 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.016 0.001 TYR C 359 PHE 0.023 0.001 PHE B 597 TRP 0.035 0.002 TRP D 742 HIS 0.004 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00346 (21884) covalent geometry : angle 0.74904 (29632) hydrogen bonds : bond 0.04159 ( 916) hydrogen bonds : angle 4.50990 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.689 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 173 MET cc_start: 0.8860 (mtm) cc_final: 0.8328 (mmt) REVERT: A 284 ASN cc_start: 0.8976 (t0) cc_final: 0.8570 (m110) REVERT: A 301 HIS cc_start: 0.9223 (m170) cc_final: 0.8817 (m90) REVERT: A 323 MET cc_start: 0.8375 (tpt) cc_final: 0.8128 (tpt) REVERT: A 405 GLU cc_start: 0.8484 (tt0) cc_final: 0.8234 (pt0) REVERT: A 418 GLU cc_start: 0.8991 (mp0) cc_final: 0.8753 (mp0) REVERT: A 423 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 448 TYR cc_start: 0.9316 (t80) cc_final: 0.8608 (t80) REVERT: A 464 ARG cc_start: 0.7103 (ttt180) cc_final: 0.5835 (ttp-170) REVERT: A 492 ILE cc_start: 0.8917 (tt) cc_final: 0.8661 (pt) REVERT: A 493 TRP cc_start: 0.7472 (m100) cc_final: 0.6632 (m100) REVERT: A 512 ASP cc_start: 0.6713 (m-30) cc_final: 0.5955 (t0) REVERT: A 572 MET cc_start: 0.9112 (mmm) cc_final: 0.8666 (mmm) REVERT: A 574 MET cc_start: 0.8095 (ppp) cc_final: 0.7027 (ppp) REVERT: A 578 MET cc_start: 0.8820 (mtp) cc_final: 0.8239 (mtm) REVERT: A 589 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8480 (mmtt) REVERT: A 632 LEU cc_start: 0.9501 (mt) cc_final: 0.9223 (mt) REVERT: B 133 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8890 (pm20) REVERT: B 141 ASP cc_start: 0.9015 (m-30) cc_final: 0.8683 (t0) REVERT: B 210 GLU cc_start: 0.9220 (tt0) cc_final: 0.8938 (tt0) REVERT: B 388 SER cc_start: 0.8171 (m) cc_final: 0.7451 (p) REVERT: B 401 ASN cc_start: 0.8164 (t0) cc_final: 0.7881 (t0) REVERT: B 423 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 448 TYR cc_start: 0.9159 (t80) cc_final: 0.8527 (t80) REVERT: B 484 LEU cc_start: 0.8843 (tp) cc_final: 0.8528 (pp) REVERT: B 492 ILE cc_start: 0.9112 (tt) cc_final: 0.8853 (pt) REVERT: B 493 TRP cc_start: 0.8000 (m100) cc_final: 0.6960 (m100) REVERT: B 529 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9123 (tm-30) REVERT: B 574 MET cc_start: 0.8082 (ppp) cc_final: 0.7099 (ppp) REVERT: B 578 MET cc_start: 0.8901 (mtp) cc_final: 0.8369 (mtm) REVERT: B 735 ASN cc_start: 0.6630 (m110) cc_final: 0.6183 (m-40) REVERT: C 141 ASP cc_start: 0.9227 (t0) cc_final: 0.8964 (t0) REVERT: C 301 HIS cc_start: 0.9348 (m170) cc_final: 0.8987 (m90) REVERT: C 388 SER cc_start: 0.8276 (m) cc_final: 0.7515 (m) REVERT: C 418 GLU cc_start: 0.9165 (mp0) cc_final: 0.8797 (mp0) REVERT: C 448 TYR cc_start: 0.9328 (t80) cc_final: 0.8570 (t80) REVERT: C 464 ARG cc_start: 0.6212 (mtt-85) cc_final: 0.5573 (tpt-90) REVERT: C 488 MET cc_start: 0.8657 (ppp) cc_final: 0.8455 (ppp) REVERT: C 529 GLN cc_start: 0.9540 (tp40) cc_final: 0.8925 (tp40) REVERT: C 550 CYS cc_start: 0.8827 (t) cc_final: 0.8539 (t) REVERT: C 557 LEU cc_start: 0.8952 (mm) cc_final: 0.8659 (tp) REVERT: C 574 MET cc_start: 0.8205 (ppp) cc_final: 0.7097 (ppp) REVERT: C 578 MET cc_start: 0.9006 (mtp) cc_final: 0.8465 (mtm) REVERT: C 632 LEU cc_start: 0.9524 (mt) cc_final: 0.9252 (mm) REVERT: D 173 MET cc_start: 0.8818 (mtm) cc_final: 0.8336 (mmm) REVERT: D 323 MET cc_start: 0.8515 (tpt) cc_final: 0.8229 (tpt) REVERT: D 415 ASN cc_start: 0.8747 (p0) cc_final: 0.8432 (p0) REVERT: D 418 GLU cc_start: 0.8815 (mp0) cc_final: 0.8463 (mp0) REVERT: D 419 MET cc_start: 0.8634 (pmm) cc_final: 0.8412 (pmm) REVERT: D 448 TYR cc_start: 0.9290 (t80) cc_final: 0.8462 (t80) REVERT: D 493 TRP cc_start: 0.7774 (m100) cc_final: 0.6839 (m100) REVERT: D 512 ASP cc_start: 0.6608 (m-30) cc_final: 0.5953 (t0) REVERT: D 548 LEU cc_start: 0.9350 (pt) cc_final: 0.9084 (mm) REVERT: D 578 MET cc_start: 0.8750 (mtp) cc_final: 0.8419 (mtm) REVERT: D 631 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 632 LEU cc_start: 0.9662 (mt) cc_final: 0.9350 (mt) REVERT: D 635 LEU cc_start: 0.9132 (mt) cc_final: 0.8873 (mt) REVERT: D 702 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 733 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7226 (mmm160) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.1322 time to fit residues: 106.3503 Evaluate side-chains 388 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 136 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 131 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 181 optimal weight: 0.0030 overall best weight: 1.5892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065408 restraints weight = 87166.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066976 restraints weight = 60647.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068113 restraints weight = 46175.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068955 restraints weight = 37513.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069408 restraints weight = 32400.986| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21884 Z= 0.135 Angle : 0.734 9.118 29632 Z= 0.367 Chirality : 0.042 0.553 3384 Planarity : 0.004 0.068 3724 Dihedral : 5.677 35.239 2864 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.20 % Favored : 86.65 % 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 : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2636 helix: 0.41 (0.13), residues: 1460 sheet: -3.80 (0.59), residues: 48 loop : -3.42 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 122 TYR 0.016 0.001 TYR A 409 PHE 0.022 0.001 PHE B 597 TRP 0.021 0.002 TRP D 742 HIS 0.002 0.000 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00286 (21884) covalent geometry : angle 0.73376 (29632) hydrogen bonds : bond 0.03967 ( 916) hydrogen bonds : angle 4.34003 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8665 (mtm) cc_final: 0.8434 (mtp) REVERT: A 301 HIS cc_start: 0.9035 (m170) cc_final: 0.8603 (m90) REVERT: A 336 MET cc_start: 0.7285 (tmm) cc_final: 0.6989 (tmm) REVERT: A 418 GLU cc_start: 0.8852 (mp0) cc_final: 0.8501 (mp0) REVERT: A 448 TYR cc_start: 0.9250 (t80) cc_final: 0.8712 (t80) REVERT: A 484 LEU cc_start: 0.8724 (tp) cc_final: 0.8466 (pp) REVERT: A 493 TRP cc_start: 0.7398 (m100) cc_final: 0.6792 (m100) REVERT: A 512 ASP cc_start: 0.6469 (m-30) cc_final: 0.5756 (t0) REVERT: A 548 LEU cc_start: 0.9113 (pt) cc_final: 0.8888 (mt) REVERT: A 572 MET cc_start: 0.9011 (mmm) cc_final: 0.8574 (mmm) REVERT: A 574 MET cc_start: 0.7908 (ppp) cc_final: 0.6958 (ppp) REVERT: A 578 MET cc_start: 0.8777 (mtp) cc_final: 0.8253 (mtm) REVERT: A 632 LEU cc_start: 0.9368 (mt) cc_final: 0.9076 (mt) REVERT: B 141 ASP cc_start: 0.8974 (m-30) cc_final: 0.8634 (t0) REVERT: B 318 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8586 (mtpt) REVERT: B 388 SER cc_start: 0.8108 (m) cc_final: 0.7512 (p) REVERT: B 401 ASN cc_start: 0.8103 (t0) cc_final: 0.7819 (t0) REVERT: B 423 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 448 TYR cc_start: 0.9159 (t80) cc_final: 0.8454 (t80) REVERT: B 484 LEU cc_start: 0.8728 (tp) cc_final: 0.8415 (pp) REVERT: B 492 ILE cc_start: 0.9095 (tt) cc_final: 0.8871 (pt) REVERT: B 493 TRP cc_start: 0.7784 (m100) cc_final: 0.6818 (m100) REVERT: B 529 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8810 (tm-30) REVERT: B 548 LEU cc_start: 0.9271 (pt) cc_final: 0.9009 (mm) REVERT: B 574 MET cc_start: 0.7938 (ppp) cc_final: 0.7019 (ppp) REVERT: B 578 MET cc_start: 0.8904 (mtp) cc_final: 0.8314 (mtm) REVERT: B 601 PHE cc_start: 0.8470 (m-80) cc_final: 0.7787 (m-80) REVERT: B 735 ASN cc_start: 0.6577 (m110) cc_final: 0.6031 (m-40) REVERT: C 141 ASP cc_start: 0.9134 (t0) cc_final: 0.8876 (t0) REVERT: C 388 SER cc_start: 0.7961 (m) cc_final: 0.7131 (m) REVERT: C 418 GLU cc_start: 0.9055 (mp0) cc_final: 0.8682 (mp0) REVERT: C 451 TYR cc_start: 0.8762 (t80) cc_final: 0.8519 (t80) REVERT: C 464 ARG cc_start: 0.6025 (mtt-85) cc_final: 0.5556 (tpt-90) REVERT: C 484 LEU cc_start: 0.8772 (tp) cc_final: 0.8540 (pp) REVERT: C 488 MET cc_start: 0.8514 (ppp) cc_final: 0.8277 (ppp) REVERT: C 529 GLN cc_start: 0.9448 (tp40) cc_final: 0.9103 (tp40) REVERT: C 574 MET cc_start: 0.8066 (ppp) cc_final: 0.6642 (ppp) REVERT: C 578 MET cc_start: 0.8886 (mtp) cc_final: 0.8405 (mtm) REVERT: C 632 LEU cc_start: 0.9421 (mt) cc_final: 0.9196 (mm) REVERT: D 173 MET cc_start: 0.8596 (mtm) cc_final: 0.8146 (mmm) REVERT: D 418 GLU cc_start: 0.8732 (mp0) cc_final: 0.8358 (mp0) REVERT: D 448 TYR cc_start: 0.9212 (t80) cc_final: 0.8546 (t80) REVERT: D 484 LEU cc_start: 0.8715 (tp) cc_final: 0.8491 (pp) REVERT: D 492 ILE cc_start: 0.8667 (tt) cc_final: 0.8347 (pt) REVERT: D 493 TRP cc_start: 0.7687 (m100) cc_final: 0.6575 (m100) REVERT: D 512 ASP cc_start: 0.6657 (m-30) cc_final: 0.5861 (t0) REVERT: D 548 LEU cc_start: 0.9292 (pt) cc_final: 0.9077 (mt) REVERT: D 572 MET cc_start: 0.9000 (mmm) cc_final: 0.8699 (mmm) REVERT: D 574 MET cc_start: 0.7946 (ppp) cc_final: 0.7194 (ppp) REVERT: D 578 MET cc_start: 0.8720 (mtp) cc_final: 0.8198 (mtm) REVERT: D 632 LEU cc_start: 0.9578 (mt) cc_final: 0.9269 (mt) REVERT: D 733 ARG cc_start: 0.7385 (mmm160) cc_final: 0.7160 (mmm160) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.1215 time to fit residues: 99.8858 Evaluate side-chains 385 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063522 restraints weight = 89317.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065110 restraints weight = 62673.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066018 restraints weight = 47694.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066807 restraints weight = 39994.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067288 restraints weight = 34940.909| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21884 Z= 0.192 Angle : 0.784 9.434 29632 Z= 0.394 Chirality : 0.044 0.776 3384 Planarity : 0.005 0.100 3724 Dihedral : 5.830 33.877 2864 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.91 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2636 helix: 0.36 (0.13), residues: 1460 sheet: -3.69 (0.63), residues: 48 loop : -3.41 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 122 TYR 0.017 0.002 TYR B 359 PHE 0.036 0.002 PHE C 526 TRP 0.020 0.002 TRP D 742 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00415 (21884) covalent geometry : angle 0.78364 (29632) hydrogen bonds : bond 0.04155 ( 916) hydrogen bonds : angle 4.56083 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8780 (mtm) cc_final: 0.8239 (mmt) REVERT: A 284 ASN cc_start: 0.8861 (t0) cc_final: 0.8543 (m-40) REVERT: A 318 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8640 (tppt) REVERT: A 418 GLU cc_start: 0.8908 (mp0) cc_final: 0.8535 (mp0) REVERT: A 419 MET cc_start: 0.8533 (pmm) cc_final: 0.8210 (pmm) REVERT: A 493 TRP cc_start: 0.7612 (m100) cc_final: 0.6949 (m100) REVERT: A 512 ASP cc_start: 0.6573 (m-30) cc_final: 0.5897 (t0) REVERT: A 548 LEU cc_start: 0.9190 (pt) cc_final: 0.8966 (mt) REVERT: A 572 MET cc_start: 0.9063 (mmm) cc_final: 0.8627 (mmm) REVERT: A 574 MET cc_start: 0.8047 (ppp) cc_final: 0.7234 (ppp) REVERT: A 578 MET cc_start: 0.8774 (mtp) cc_final: 0.8291 (mtm) REVERT: A 590 PHE cc_start: 0.8975 (t80) cc_final: 0.8762 (t80) REVERT: A 632 LEU cc_start: 0.9465 (mt) cc_final: 0.9191 (mt) REVERT: A 730 LEU cc_start: 0.9254 (pt) cc_final: 0.9042 (pt) REVERT: B 141 ASP cc_start: 0.8962 (m-30) cc_final: 0.8574 (t0) REVERT: B 336 MET cc_start: 0.7795 (ppp) cc_final: 0.7544 (ppp) REVERT: B 388 SER cc_start: 0.8260 (m) cc_final: 0.7530 (p) REVERT: B 401 ASN cc_start: 0.8180 (t0) cc_final: 0.7872 (t0) REVERT: B 423 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 448 TYR cc_start: 0.9231 (t80) cc_final: 0.8497 (t80) REVERT: B 484 LEU cc_start: 0.8794 (tp) cc_final: 0.8479 (pp) REVERT: B 492 ILE cc_start: 0.9094 (tt) cc_final: 0.8860 (pt) REVERT: B 493 TRP cc_start: 0.7936 (m100) cc_final: 0.6959 (m100) REVERT: B 529 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9156 (tm-30) REVERT: B 578 MET cc_start: 0.8815 (mtp) cc_final: 0.8475 (mtm) REVERT: B 735 ASN cc_start: 0.6885 (m110) cc_final: 0.6367 (m-40) REVERT: C 141 ASP cc_start: 0.9218 (t0) cc_final: 0.8944 (t0) REVERT: C 388 SER cc_start: 0.8091 (m) cc_final: 0.7159 (m) REVERT: C 418 GLU cc_start: 0.9054 (mp0) cc_final: 0.8674 (mp0) REVERT: C 464 ARG cc_start: 0.6105 (mtt-85) cc_final: 0.5518 (tpt-90) REVERT: C 488 MET cc_start: 0.8551 (ppp) cc_final: 0.8324 (ppp) REVERT: C 493 TRP cc_start: 0.7596 (m100) cc_final: 0.6593 (m100) REVERT: C 529 GLN cc_start: 0.9554 (tp40) cc_final: 0.8899 (tp40) REVERT: C 557 LEU cc_start: 0.8994 (mm) cc_final: 0.8738 (tp) REVERT: C 574 MET cc_start: 0.8076 (ppp) cc_final: 0.6858 (ppp) REVERT: C 578 MET cc_start: 0.8856 (mtp) cc_final: 0.8431 (mtm) REVERT: C 632 LEU cc_start: 0.9522 (mt) cc_final: 0.9241 (mm) REVERT: C 730 LEU cc_start: 0.9008 (pt) cc_final: 0.8765 (pt) REVERT: D 173 MET cc_start: 0.8723 (mtm) cc_final: 0.8357 (mmt) REVERT: D 323 MET cc_start: 0.8428 (tpt) cc_final: 0.8200 (tpt) REVERT: D 418 GLU cc_start: 0.8804 (mp0) cc_final: 0.8562 (mp0) REVERT: D 493 TRP cc_start: 0.7711 (m100) cc_final: 0.6745 (m100) REVERT: D 512 ASP cc_start: 0.6582 (m-30) cc_final: 0.5869 (t0) REVERT: D 548 LEU cc_start: 0.9338 (pt) cc_final: 0.9121 (mt) REVERT: D 555 MET cc_start: 0.9072 (tpp) cc_final: 0.8488 (tpt) REVERT: D 572 MET cc_start: 0.9045 (mmm) cc_final: 0.8731 (mmm) REVERT: D 578 MET cc_start: 0.8747 (mtp) cc_final: 0.8396 (mtm) REVERT: D 733 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7232 (mmm160) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1258 time to fit residues: 94.9640 Evaluate side-chains 368 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065172 restraints weight = 87786.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066726 restraints weight = 61396.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067835 restraints weight = 46970.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068657 restraints weight = 38396.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069113 restraints weight = 33486.129| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21884 Z= 0.142 Angle : 0.759 9.550 29632 Z= 0.375 Chirality : 0.042 0.474 3384 Planarity : 0.004 0.080 3724 Dihedral : 5.621 32.465 2864 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.81 % Favored : 86.04 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.17), residues: 2636 helix: 0.44 (0.14), residues: 1456 sheet: -1.91 (0.90), residues: 28 loop : -3.51 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 118 TYR 0.012 0.001 TYR A 451 PHE 0.031 0.001 PHE C 597 TRP 0.020 0.002 TRP B 739 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00306 (21884) covalent geometry : angle 0.75949 (29632) hydrogen bonds : bond 0.03989 ( 916) hydrogen bonds : angle 4.46210 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASN cc_start: 0.8739 (t0) cc_final: 0.8471 (m110) REVERT: A 318 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8480 (tppt) REVERT: A 418 GLU cc_start: 0.8719 (mp0) cc_final: 0.8459 (mp0) REVERT: A 493 TRP cc_start: 0.7515 (m100) cc_final: 0.6621 (m100) REVERT: A 512 ASP cc_start: 0.6573 (m-30) cc_final: 0.5880 (t0) REVERT: A 548 LEU cc_start: 0.9114 (pt) cc_final: 0.8874 (mt) REVERT: A 572 MET cc_start: 0.8956 (mmm) cc_final: 0.8521 (mmm) REVERT: A 574 MET cc_start: 0.7868 (ppp) cc_final: 0.7071 (ppp) REVERT: A 578 MET cc_start: 0.8762 (mtp) cc_final: 0.8429 (mtm) REVERT: A 590 PHE cc_start: 0.8806 (t80) cc_final: 0.8602 (t80) REVERT: A 632 LEU cc_start: 0.9373 (mt) cc_final: 0.9090 (mt) REVERT: B 134 GLU cc_start: 0.8692 (pm20) cc_final: 0.8463 (pm20) REVERT: B 141 ASP cc_start: 0.8907 (m-30) cc_final: 0.8557 (t0) REVERT: B 318 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8576 (tppt) REVERT: B 323 MET cc_start: 0.8125 (tpt) cc_final: 0.7812 (tpt) REVERT: B 388 SER cc_start: 0.8225 (m) cc_final: 0.7329 (p) REVERT: B 423 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 448 TYR cc_start: 0.9227 (t80) cc_final: 0.8530 (t80) REVERT: B 484 LEU cc_start: 0.8708 (tp) cc_final: 0.8375 (pp) REVERT: B 492 ILE cc_start: 0.9115 (tt) cc_final: 0.8914 (pt) REVERT: B 493 TRP cc_start: 0.7769 (m100) cc_final: 0.6767 (m100) REVERT: B 529 GLN cc_start: 0.9398 (tm-30) cc_final: 0.8870 (tm-30) REVERT: B 548 LEU cc_start: 0.9267 (pt) cc_final: 0.9046 (mm) REVERT: B 561 ASN cc_start: 0.8740 (m-40) cc_final: 0.8431 (m-40) REVERT: B 578 MET cc_start: 0.8708 (mtp) cc_final: 0.8219 (mtm) REVERT: B 735 ASN cc_start: 0.6875 (m110) cc_final: 0.6375 (m-40) REVERT: C 141 ASP cc_start: 0.9162 (t0) cc_final: 0.8879 (t0) REVERT: C 388 SER cc_start: 0.7900 (m) cc_final: 0.6947 (m) REVERT: C 418 GLU cc_start: 0.8955 (mp0) cc_final: 0.8592 (mp0) REVERT: C 448 TYR cc_start: 0.9168 (t80) cc_final: 0.8939 (t80) REVERT: C 464 ARG cc_start: 0.6176 (mtt-85) cc_final: 0.5836 (tpt-90) REVERT: C 493 TRP cc_start: 0.7161 (m100) cc_final: 0.6296 (m100) REVERT: C 529 GLN cc_start: 0.9391 (tp40) cc_final: 0.9019 (tp40) REVERT: C 555 MET cc_start: 0.8708 (mtp) cc_final: 0.8483 (tpp) REVERT: C 574 MET cc_start: 0.8078 (ppp) cc_final: 0.7778 (ppp) REVERT: C 632 LEU cc_start: 0.9443 (mt) cc_final: 0.9183 (mm) REVERT: D 173 MET cc_start: 0.8612 (mtm) cc_final: 0.8248 (mmt) REVERT: D 493 TRP cc_start: 0.7680 (m100) cc_final: 0.6780 (m100) REVERT: D 512 ASP cc_start: 0.6564 (m-30) cc_final: 0.5826 (t0) REVERT: D 548 LEU cc_start: 0.9255 (pt) cc_final: 0.9033 (mt) REVERT: D 555 MET cc_start: 0.8919 (tpp) cc_final: 0.8555 (tpt) REVERT: D 572 MET cc_start: 0.8946 (mmm) cc_final: 0.8676 (mmm) REVERT: D 578 MET cc_start: 0.8690 (mtp) cc_final: 0.8244 (mtm) REVERT: D 733 ARG cc_start: 0.7331 (mmm160) cc_final: 0.7108 (mmm160) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1259 time to fit residues: 94.7754 Evaluate side-chains 375 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.080700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064866 restraints weight = 85916.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066398 restraints weight = 61693.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067282 restraints weight = 47256.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068072 restraints weight = 39425.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068537 restraints weight = 34226.803| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21884 Z= 0.148 Angle : 0.776 14.012 29632 Z= 0.384 Chirality : 0.042 0.380 3384 Planarity : 0.005 0.075 3724 Dihedral : 5.642 32.957 2864 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.42 % Favored : 85.43 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2636 helix: 0.42 (0.13), residues: 1452 sheet: -3.96 (0.58), residues: 52 loop : -3.41 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 118 TYR 0.017 0.001 TYR D 594 PHE 0.029 0.001 PHE C 597 TRP 0.022 0.002 TRP B 739 HIS 0.014 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00326 (21884) covalent geometry : angle 0.77570 (29632) hydrogen bonds : bond 0.04045 ( 916) hydrogen bonds : angle 4.49547 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASN cc_start: 0.8776 (t0) cc_final: 0.8501 (m-40) REVERT: A 318 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8505 (tppt) REVERT: A 493 TRP cc_start: 0.7424 (m100) cc_final: 0.6756 (m100) REVERT: A 548 LEU cc_start: 0.9127 (pt) cc_final: 0.8883 (mt) REVERT: A 572 MET cc_start: 0.8898 (mmm) cc_final: 0.8539 (mmm) REVERT: A 574 MET cc_start: 0.7876 (ppp) cc_final: 0.7120 (ppp) REVERT: A 578 MET cc_start: 0.8875 (mtp) cc_final: 0.8242 (mtm) REVERT: A 632 LEU cc_start: 0.9383 (mt) cc_final: 0.9109 (mt) REVERT: B 134 GLU cc_start: 0.8641 (pm20) cc_final: 0.8383 (pm20) REVERT: B 141 ASP cc_start: 0.8919 (m-30) cc_final: 0.8569 (t70) REVERT: B 318 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8564 (tppt) REVERT: B 323 MET cc_start: 0.8044 (tpt) cc_final: 0.7841 (tpt) REVERT: B 380 TRP cc_start: 0.7377 (t-100) cc_final: 0.7132 (t-100) REVERT: B 388 SER cc_start: 0.8278 (m) cc_final: 0.7396 (p) REVERT: B 423 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 448 TYR cc_start: 0.9238 (t80) cc_final: 0.8919 (t80) REVERT: B 484 LEU cc_start: 0.8712 (tp) cc_final: 0.8377 (pp) REVERT: B 526 PHE cc_start: 0.8615 (m-10) cc_final: 0.8414 (m-10) REVERT: B 529 GLN cc_start: 0.9424 (tm-30) cc_final: 0.8892 (tm-30) REVERT: B 561 ASN cc_start: 0.8750 (m-40) cc_final: 0.8542 (m-40) REVERT: B 578 MET cc_start: 0.8699 (mtp) cc_final: 0.8451 (mtm) REVERT: B 735 ASN cc_start: 0.6976 (m110) cc_final: 0.6443 (m-40) REVERT: C 141 ASP cc_start: 0.9150 (t0) cc_final: 0.8869 (t0) REVERT: C 388 SER cc_start: 0.7871 (m) cc_final: 0.6770 (m) REVERT: C 418 GLU cc_start: 0.8914 (mp0) cc_final: 0.8566 (mp0) REVERT: C 464 ARG cc_start: 0.6124 (mtt-85) cc_final: 0.5761 (tpt-90) REVERT: C 493 TRP cc_start: 0.7208 (m100) cc_final: 0.6893 (m100) REVERT: C 529 GLN cc_start: 0.9409 (tp40) cc_final: 0.9091 (tp40) REVERT: C 555 MET cc_start: 0.8834 (mtp) cc_final: 0.8604 (tpp) REVERT: C 574 MET cc_start: 0.8089 (ppp) cc_final: 0.7732 (ppp) REVERT: C 578 MET cc_start: 0.7955 (tmm) cc_final: 0.7473 (tmm) REVERT: C 632 LEU cc_start: 0.9456 (mt) cc_final: 0.9098 (mt) REVERT: D 173 MET cc_start: 0.8625 (mtm) cc_final: 0.8225 (mmt) REVERT: D 492 ILE cc_start: 0.8874 (tt) cc_final: 0.8646 (pt) REVERT: D 493 TRP cc_start: 0.7796 (m100) cc_final: 0.6743 (m100) REVERT: D 512 ASP cc_start: 0.6573 (m-30) cc_final: 0.5865 (t0) REVERT: D 555 MET cc_start: 0.8921 (tpp) cc_final: 0.8557 (tpt) REVERT: D 572 MET cc_start: 0.8965 (mmm) cc_final: 0.8647 (mmm) REVERT: D 578 MET cc_start: 0.8714 (mtp) cc_final: 0.8315 (mtm) REVERT: D 598 LEU cc_start: 0.9324 (mt) cc_final: 0.8995 (mt) REVERT: D 733 ARG cc_start: 0.7477 (mmm160) cc_final: 0.7253 (mmm160) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1242 time to fit residues: 92.8284 Evaluate side-chains 372 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 580 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066326 restraints weight = 85191.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067781 restraints weight = 60807.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068976 restraints weight = 46966.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069497 restraints weight = 37939.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070144 restraints weight = 33444.484| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21884 Z= 0.131 Angle : 0.761 11.681 29632 Z= 0.371 Chirality : 0.041 0.302 3384 Planarity : 0.004 0.073 3724 Dihedral : 5.422 29.727 2864 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.24 % Favored : 86.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2636 helix: 0.48 (0.14), residues: 1452 sheet: -4.01 (0.57), residues: 52 loop : -3.39 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 118 TYR 0.014 0.001 TYR C 547 PHE 0.027 0.001 PHE C 597 TRP 0.017 0.002 TRP D 742 HIS 0.005 0.000 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00285 (21884) covalent geometry : angle 0.76068 (29632) hydrogen bonds : bond 0.03809 ( 916) hydrogen bonds : angle 4.36128 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.97 seconds wall clock time: 54 minutes 32.88 seconds (3272.88 seconds total)