Starting phenix.real_space_refine on Thu Mar 5 09:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvp_20496/03_2026/6pvp_20496.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvp_20496/03_2026/6pvp_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_20496/03_2026/6pvp_20496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvp_20496/03_2026/6pvp_20496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvp_20496/03_2026/6pvp_20496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvp_20496/03_2026/6pvp_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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21425 Number of models: 1 Model: "" Number of chains: 5 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: "B" 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: "C" 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: "D" 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} Time building chain proxies: 4.93, per 1000 atoms: 0.23 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: 1.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.59 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: 2.21 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.900 Find NCS groups from input model: 0.410 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- 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 : 0.860 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: 0.8084 (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: 0.8451 (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: 0.8539 (t) REVERT: C 572 MET cc_start: 0.8917 (mmt) cc_final: 0.8629 (mmm) REVERT: C 574 MET cc_start: 0.7862 (ppp) cc_final: 0.6539 (ppp) REVERT: C 578 MET cc_start: 0.8797 (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: 0.8360 (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: 0.1603 time to fit residues: 173.5333 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 : 0.810 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065786 restraints weight = 88036.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067287 restraints weight = 61445.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068379 restraints weight = 46793.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069034 restraints weight = 38353.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069627 restraints weight = 33455.888| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.838 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: 0.8957 (pm20) cc_final: 0.8711 (pm20) REVERT: A 156 ASP cc_start: 0.9115 (m-30) cc_final: 0.8862 (m-30) REVERT: A 173 MET cc_start: 0.8888 (mtm) cc_final: 0.8311 (mmm) REVERT: A 321 TYR cc_start: 0.8950 (t80) cc_final: 0.8315 (t80) REVERT: A 418 GLU cc_start: 0.9128 (mp0) cc_final: 0.8793 (mp0) REVERT: A 423 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 448 TYR cc_start: 0.8663 (t80) cc_final: 0.8294 (t80) REVERT: A 464 ARG cc_start: 0.7360 (ttt180) cc_final: 0.6898 (ttt180) REVERT: A 493 TRP cc_start: 0.7355 (m100) cc_final: 0.6986 (m100) REVERT: A 512 ASP cc_start: 0.6400 (m-30) cc_final: 0.5798 (t0) REVERT: A 550 CYS cc_start: 0.9060 (t) cc_final: 0.8799 (t) REVERT: A 574 MET cc_start: 0.8410 (ppp) cc_final: 0.7173 (ppp) REVERT: A 578 MET cc_start: 0.8774 (mtp) cc_final: 0.8202 (mtt) REVERT: A 702 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 124 PHE cc_start: 0.8669 (m-10) cc_final: 0.8267 (m-80) REVERT: B 134 GLU cc_start: 0.8954 (pm20) cc_final: 0.8710 (pm20) REVERT: B 173 MET cc_start: 0.8741 (mtt) cc_final: 0.8462 (mmm) REVERT: B 234 LEU cc_start: 0.9429 (mm) cc_final: 0.9170 (mm) REVERT: B 271 CYS cc_start: 0.9461 (m) cc_final: 0.9030 (t) REVERT: B 423 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 448 TYR cc_start: 0.8820 (t80) cc_final: 0.7787 (t80) REVERT: B 451 TYR cc_start: 0.8913 (t80) cc_final: 0.8650 (t80) REVERT: B 484 LEU cc_start: 0.8721 (tp) cc_final: 0.8499 (tp) REVERT: B 493 TRP cc_start: 0.7573 (m100) cc_final: 0.6555 (m100) REVERT: B 529 GLN cc_start: 0.9396 (tm-30) cc_final: 0.9012 (tm-30) REVERT: B 550 CYS cc_start: 0.8776 (t) cc_final: 0.8500 (t) REVERT: B 555 MET cc_start: 0.8876 (ttt) cc_final: 0.8581 (ttt) REVERT: B 574 MET cc_start: 0.7972 (ppp) cc_final: 0.7120 (ppp) REVERT: B 578 MET cc_start: 0.8978 (mtp) cc_final: 0.8548 (mtm) REVERT: B 687 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 158 LEU cc_start: 0.9474 (tt) cc_final: 0.9218 (pp) REVERT: C 173 MET cc_start: 0.8702 (mmp) cc_final: 0.7904 (mmp) REVERT: C 323 MET cc_start: 0.8887 (ttm) cc_final: 0.8583 (tpt) REVERT: C 388 SER cc_start: 0.8293 (m) cc_final: 0.7470 (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: 0.9461 (tm-30) cc_final: 0.9078 (tm-30) REVERT: C 550 CYS cc_start: 0.8946 (t) cc_final: 0.8730 (t) REVERT: C 574 MET cc_start: 0.8053 (ppp) cc_final: 0.7087 (ppp) REVERT: C 578 MET cc_start: 0.8917 (mtp) cc_final: 0.8232 (mtm) REVERT: C 632 LEU cc_start: 0.9417 (mt) cc_final: 0.9104 (mm) REVERT: C 735 ASN cc_start: 0.7883 (m110) cc_final: 0.7592 (m110) REVERT: D 120 LYS cc_start: 0.9428 (tttt) cc_final: 0.9204 (ptpt) REVERT: D 131 CYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7446 (p) REVERT: D 134 GLU cc_start: 0.8913 (pm20) cc_final: 0.8494 (pm20) REVERT: D 156 ASP cc_start: 0.9095 (m-30) cc_final: 0.8832 (m-30) REVERT: D 173 MET cc_start: 0.8775 (mtm) cc_final: 0.8416 (mmm) REVERT: D 321 TYR cc_start: 0.8982 (t80) cc_final: 0.8403 (t80) REVERT: D 418 GLU cc_start: 0.8936 (mp0) cc_final: 0.8569 (mp0) REVERT: D 448 TYR cc_start: 0.8672 (t80) cc_final: 0.8294 (t80) REVERT: D 451 TYR cc_start: 0.8735 (t80) cc_final: 0.8535 (t80) REVERT: D 493 TRP cc_start: 0.7433 (m100) cc_final: 0.6298 (m100) REVERT: D 512 ASP cc_start: 0.6151 (m-30) cc_final: 0.5707 (t0) REVERT: D 550 CYS cc_start: 0.8799 (t) cc_final: 0.8563 (t) REVERT: D 574 MET cc_start: 0.8154 (ppp) cc_final: 0.7621 (ppp) REVERT: D 578 MET cc_start: 0.8753 (mtp) cc_final: 0.8068 (mtm) REVERT: D 631 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7905 (tm-30) REVERT: D 702 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7913 (tm-30) outliers start: 4 outliers final: 0 residues processed: 574 average time/residue: 0.1451 time to fit residues: 131.4999 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 : 0.833 ------------------------------------------------------------------------------- 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: 2.9990 chunk 250 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.0570 chunk 256 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.5304 ------------------------------------------------------------------------------- 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 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 ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065127 restraints weight = 88587.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066931 restraints weight = 59886.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067999 restraints weight = 44703.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068892 restraints weight = 36356.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069597 restraints weight = 31216.037| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21884 Z= 0.185 Angle : 0.760 9.895 29632 Z= 0.391 Chirality : 0.042 0.175 3384 Planarity : 0.004 0.049 3724 Dihedral : 6.313 38.423 2864 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.30 % Favored : 85.55 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -2.36 (0.16), residues: 2636 helix: -0.14 (0.13), residues: 1456 sheet: -4.54 (0.42), residues: 48 loop : -3.48 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 464 TYR 0.018 0.002 TYR D 359 PHE 0.043 0.002 PHE C 526 TRP 0.019 0.002 TRP D 521 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00383 (21884) covalent geometry : angle 0.76017 (29632) hydrogen bonds : bond 0.04788 ( 916) hydrogen bonds : angle 4.62604 ( 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 515 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.902 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 124 PHE cc_start: 0.8831 (m-80) cc_final: 0.8436 (m-80) REVERT: A 173 MET cc_start: 0.8678 (mtm) cc_final: 0.8280 (mmm) REVERT: A 301 HIS cc_start: 0.9175 (m170) cc_final: 0.8823 (m-70) REVERT: A 321 TYR cc_start: 0.8841 (t80) cc_final: 0.8124 (t80) REVERT: A 418 GLU cc_start: 0.9095 (mp0) cc_final: 0.8641 (mp0) REVERT: A 423 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 448 TYR cc_start: 0.9083 (t80) cc_final: 0.8747 (t80) REVERT: A 493 TRP cc_start: 0.7470 (m100) cc_final: 0.6885 (m100) REVERT: A 512 ASP cc_start: 0.6441 (m-30) cc_final: 0.5871 (t0) REVERT: A 574 MET cc_start: 0.8169 (ppp) cc_final: 0.7456 (ppp) REVERT: A 578 MET cc_start: 0.8716 (mtp) cc_final: 0.8205 (mtm) REVERT: A 702 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 730 LEU cc_start: 0.9284 (pt) cc_final: 0.9083 (pt) REVERT: B 124 PHE cc_start: 0.8517 (m-10) cc_final: 0.8159 (m-80) REVERT: B 134 GLU cc_start: 0.8600 (pm20) cc_final: 0.8374 (pm20) REVERT: B 173 MET cc_start: 0.8749 (mtt) cc_final: 0.8454 (mmm) REVERT: B 210 GLU cc_start: 0.9148 (tt0) cc_final: 0.8841 (tt0) REVERT: B 423 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 448 TYR cc_start: 0.8911 (t80) cc_final: 0.7953 (t80) REVERT: B 493 TRP cc_start: 0.7850 (m100) cc_final: 0.7067 (m100) REVERT: B 550 CYS cc_start: 0.8800 (t) cc_final: 0.8576 (t) REVERT: B 572 MET cc_start: 0.9305 (mmm) cc_final: 0.9056 (mmm) REVERT: B 574 MET cc_start: 0.7993 (ppp) cc_final: 0.7269 (ppp) REVERT: B 578 MET cc_start: 0.8925 (mtp) cc_final: 0.8410 (mtm) REVERT: B 687 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 735 ASN cc_start: 0.6578 (m110) cc_final: 0.6094 (m110) REVERT: C 141 ASP cc_start: 0.9225 (t0) cc_final: 0.8997 (t0) REVERT: C 158 LEU cc_start: 0.9419 (tt) cc_final: 0.9215 (pp) REVERT: C 173 MET cc_start: 0.8532 (mmp) cc_final: 0.8222 (mmp) REVERT: C 303 LEU cc_start: 0.9624 (mp) cc_final: 0.9328 (tp) REVERT: C 388 SER cc_start: 0.8164 (m) cc_final: 0.7732 (m) REVERT: C 448 TYR cc_start: 0.9092 (t80) cc_final: 0.8453 (t80) REVERT: C 455 LEU cc_start: 0.9674 (tp) cc_final: 0.9362 (tp) REVERT: C 464 ARG cc_start: 0.6451 (mtt-85) cc_final: 0.5774 (tpt-90) REVERT: C 529 GLN cc_start: 0.9403 (tm-30) cc_final: 0.9203 (tm-30) REVERT: C 574 MET cc_start: 0.7849 (ppp) cc_final: 0.7028 (ppp) REVERT: C 578 MET cc_start: 0.8922 (mtp) cc_final: 0.8498 (mtm) REVERT: C 632 LEU cc_start: 0.9433 (mt) cc_final: 0.9102 (mm) REVERT: C 687 GLU cc_start: 0.8838 (tt0) cc_final: 0.8561 (tm-30) REVERT: D 120 LYS cc_start: 0.9417 (tttt) cc_final: 0.9092 (ptpt) REVERT: D 173 MET cc_start: 0.8698 (mtm) cc_final: 0.8349 (mmm) REVERT: D 301 HIS cc_start: 0.9185 (m170) cc_final: 0.8839 (m-70) REVERT: D 323 MET cc_start: 0.8667 (tpt) cc_final: 0.8098 (tpt) REVERT: D 405 GLU cc_start: 0.8503 (tt0) cc_final: 0.8191 (mt-10) REVERT: D 418 GLU cc_start: 0.8898 (mp0) cc_final: 0.8466 (mp0) REVERT: D 448 TYR cc_start: 0.9022 (t80) cc_final: 0.8615 (t80) REVERT: D 451 TYR cc_start: 0.8873 (t80) cc_final: 0.8667 (t80) REVERT: D 455 LEU cc_start: 0.9466 (tp) cc_final: 0.9034 (tp) REVERT: D 493 TRP cc_start: 0.7376 (m100) cc_final: 0.6331 (m100) REVERT: D 512 ASP cc_start: 0.6425 (m-30) cc_final: 0.5883 (t0) REVERT: D 548 LEU cc_start: 0.9259 (tp) cc_final: 0.8997 (pt) REVERT: D 578 MET cc_start: 0.8747 (mtp) cc_final: 0.8516 (mtt) REVERT: D 631 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7927 (tm-30) REVERT: D 632 LEU cc_start: 0.9532 (mm) cc_final: 0.9206 (mt) REVERT: D 635 LEU cc_start: 0.9295 (mt) cc_final: 0.8993 (mt) REVERT: D 661 TYR cc_start: 0.8688 (t80) cc_final: 0.8472 (t80) REVERT: D 702 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8040 (tm-30) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.1371 time to fit residues: 113.3953 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 : 0.785 ------------------------------------------------------------------------------- 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: 7.9990 chunk 6 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 114 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 585 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063325 restraints weight = 89491.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065071 restraints weight = 59851.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.066313 restraints weight = 44527.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067110 restraints weight = 35873.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067515 restraints weight = 30893.088| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21884 Z= 0.200 Angle : 0.773 10.846 29632 Z= 0.397 Chirality : 0.042 0.169 3384 Planarity : 0.005 0.091 3724 Dihedral : 6.212 38.311 2864 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.34 % Favored : 85.51 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -2.18 (0.16), residues: 2636 helix: 0.03 (0.13), residues: 1480 sheet: -4.21 (0.48), residues: 48 loop : -3.51 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 714 TYR 0.018 0.002 TYR D 359 PHE 0.024 0.002 PHE B 597 TRP 0.024 0.002 TRP C 521 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00425 (21884) covalent geometry : angle 0.77288 (29632) hydrogen bonds : bond 0.04539 ( 916) hydrogen bonds : angle 4.62593 ( 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 504 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.857 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: 0.8736 (mtm) cc_final: 0.8312 (mmm) REVERT: A 323 MET cc_start: 0.8532 (tpt) cc_final: 0.8028 (tpt) REVERT: A 405 GLU cc_start: 0.8498 (tt0) cc_final: 0.8170 (pt0) REVERT: A 418 GLU cc_start: 0.9019 (mp0) cc_final: 0.8569 (mp0) REVERT: A 423 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 448 TYR cc_start: 0.9200 (t80) cc_final: 0.8410 (t80) REVERT: A 451 TYR cc_start: 0.9063 (t80) cc_final: 0.8861 (t80) REVERT: A 493 TRP cc_start: 0.7390 (m100) cc_final: 0.6815 (m100) REVERT: A 512 ASP cc_start: 0.6503 (m-30) cc_final: 0.5884 (t0) REVERT: A 574 MET cc_start: 0.8240 (ppp) cc_final: 0.7126 (ppp) REVERT: A 578 MET cc_start: 0.8866 (mtp) cc_final: 0.8289 (mtm) REVERT: A 589 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8594 (mmtt) REVERT: A 594 TYR cc_start: 0.7614 (t80) cc_final: 0.7348 (t80) REVERT: A 702 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 133 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8862 (pm20) REVERT: B 141 ASP cc_start: 0.9084 (m-30) cc_final: 0.8756 (t0) REVERT: B 210 GLU cc_start: 0.9190 (tt0) cc_final: 0.8921 (tt0) REVERT: B 423 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 448 TYR cc_start: 0.8989 (t80) cc_final: 0.8451 (t80) REVERT: B 493 TRP cc_start: 0.7892 (m100) cc_final: 0.6964 (m100) REVERT: B 550 CYS cc_start: 0.8838 (t) cc_final: 0.8561 (t) REVERT: B 574 MET cc_start: 0.8164 (ppp) cc_final: 0.7266 (ppp) REVERT: B 578 MET cc_start: 0.9046 (mtp) cc_final: 0.8447 (mtm) REVERT: B 735 ASN cc_start: 0.6708 (m110) cc_final: 0.6227 (m110) REVERT: C 141 ASP cc_start: 0.9232 (t0) cc_final: 0.8988 (t0) REVERT: C 158 LEU cc_start: 0.9426 (tt) cc_final: 0.9211 (pp) REVERT: C 173 MET cc_start: 0.8594 (mmp) cc_final: 0.8175 (mmp) REVERT: C 303 LEU cc_start: 0.9646 (mp) cc_final: 0.9392 (tp) REVERT: C 323 MET cc_start: 0.8996 (tmm) cc_final: 0.8779 (tmm) REVERT: C 388 SER cc_start: 0.8231 (m) cc_final: 0.7443 (m) REVERT: C 455 LEU cc_start: 0.9662 (tp) cc_final: 0.9369 (tp) REVERT: C 464 ARG cc_start: 0.6270 (mtt-85) cc_final: 0.5693 (ttt180) REVERT: C 550 CYS cc_start: 0.8697 (t) cc_final: 0.8395 (t) REVERT: C 574 MET cc_start: 0.8091 (ppp) cc_final: 0.6842 (ppp) REVERT: C 578 MET cc_start: 0.8988 (mtp) cc_final: 0.8329 (mtm) REVERT: C 632 LEU cc_start: 0.9489 (mt) cc_final: 0.9211 (mm) REVERT: C 687 GLU cc_start: 0.8770 (tt0) cc_final: 0.8545 (tm-30) REVERT: D 173 MET cc_start: 0.8812 (mtm) cc_final: 0.8302 (mmt) REVERT: D 210 GLU cc_start: 0.9286 (tt0) cc_final: 0.9053 (tt0) REVERT: D 318 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8715 (tppt) REVERT: D 323 MET cc_start: 0.8617 (tpt) cc_final: 0.8299 (tpt) REVERT: D 418 GLU cc_start: 0.8911 (mp0) cc_final: 0.8457 (mp0) REVERT: D 451 TYR cc_start: 0.8921 (t80) cc_final: 0.8649 (t80) REVERT: D 493 TRP cc_start: 0.7496 (m100) cc_final: 0.6550 (m100) REVERT: D 512 ASP cc_start: 0.6506 (m-30) cc_final: 0.5861 (t0) REVERT: D 550 CYS cc_start: 0.8897 (t) cc_final: 0.8615 (t) REVERT: D 572 MET cc_start: 0.9116 (mmm) cc_final: 0.8866 (mmm) REVERT: D 578 MET cc_start: 0.8825 (mtp) cc_final: 0.8538 (mtt) REVERT: D 702 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 730 LEU cc_start: 0.9206 (pt) cc_final: 0.8991 (pt) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1367 time to fit residues: 111.3669 Evaluate side-chains 378 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 231 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063879 restraints weight = 87148.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065287 restraints weight = 61229.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066372 restraints weight = 47274.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067102 restraints weight = 38543.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067640 restraints weight = 33398.985| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21884 Z= 0.180 Angle : 0.756 9.185 29632 Z= 0.387 Chirality : 0.042 0.158 3384 Planarity : 0.004 0.064 3724 Dihedral : 6.082 38.608 2864 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.30 % Favored : 85.55 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: -2.04 (0.16), residues: 2636 helix: 0.16 (0.13), residues: 1480 sheet: -3.95 (0.55), residues: 48 loop : -3.49 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.026 0.002 TYR D 594 PHE 0.024 0.001 PHE B 597 TRP 0.022 0.002 TRP A 521 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00387 (21884) covalent geometry : angle 0.75628 (29632) hydrogen bonds : bond 0.04369 ( 916) hydrogen bonds : angle 4.57386 ( 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 501 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.852 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: 0.8635 (mtm) cc_final: 0.8141 (mmm) REVERT: A 423 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 448 TYR cc_start: 0.9260 (t80) cc_final: 0.8878 (t80) REVERT: A 455 LEU cc_start: 0.9379 (tp) cc_final: 0.9175 (tp) REVERT: A 493 TRP cc_start: 0.7306 (m100) cc_final: 0.6751 (m100) REVERT: A 512 ASP cc_start: 0.6628 (m-30) cc_final: 0.5897 (t0) REVERT: A 548 LEU cc_start: 0.9177 (pt) cc_final: 0.8857 (mm) REVERT: A 574 MET cc_start: 0.8035 (ppp) cc_final: 0.7311 (ppp) REVERT: A 578 MET cc_start: 0.8732 (mtp) cc_final: 0.8085 (mtm) REVERT: A 632 LEU cc_start: 0.9337 (mt) cc_final: 0.8971 (mt) REVERT: B 133 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8746 (pm20) REVERT: B 141 ASP cc_start: 0.8980 (m-30) cc_final: 0.8686 (t0) REVERT: B 388 SER cc_start: 0.8283 (m) cc_final: 0.7580 (p) REVERT: B 423 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 493 TRP cc_start: 0.7736 (m100) cc_final: 0.7066 (m100) REVERT: B 574 MET cc_start: 0.7939 (ppp) cc_final: 0.6933 (ppp) REVERT: B 578 MET cc_start: 0.8832 (mtp) cc_final: 0.8076 (mtm) REVERT: B 735 ASN cc_start: 0.6920 (m110) cc_final: 0.6479 (m-40) REVERT: C 141 ASP cc_start: 0.9111 (t0) cc_final: 0.8881 (t0) REVERT: C 388 SER cc_start: 0.8317 (m) cc_final: 0.7570 (m) REVERT: C 418 GLU cc_start: 0.9203 (mp0) cc_final: 0.8799 (mp0) REVERT: C 453 ILE cc_start: 0.9329 (mm) cc_final: 0.9108 (tp) REVERT: C 455 LEU cc_start: 0.9596 (tp) cc_final: 0.9039 (tp) REVERT: C 464 ARG cc_start: 0.6487 (mtt-85) cc_final: 0.5836 (ttt180) REVERT: C 529 GLN cc_start: 0.9313 (tp40) cc_final: 0.9023 (tp40) REVERT: C 550 CYS cc_start: 0.8655 (t) cc_final: 0.8418 (t) REVERT: C 574 MET cc_start: 0.7870 (ppp) cc_final: 0.6719 (ppp) REVERT: C 578 MET cc_start: 0.8845 (mtp) cc_final: 0.8384 (mtm) REVERT: C 594 TYR cc_start: 0.7630 (t80) cc_final: 0.7418 (t80) REVERT: C 632 LEU cc_start: 0.9483 (mt) cc_final: 0.9180 (mm) REVERT: D 173 MET cc_start: 0.8715 (mtm) cc_final: 0.8226 (mmm) REVERT: D 210 GLU cc_start: 0.9068 (tt0) cc_final: 0.8799 (tm-30) REVERT: D 323 MET cc_start: 0.8295 (tpt) cc_final: 0.8089 (tpt) REVERT: D 336 MET cc_start: 0.7379 (ppp) cc_final: 0.7096 (tmm) REVERT: D 418 GLU cc_start: 0.8705 (mp0) cc_final: 0.8408 (mp0) REVERT: D 448 TYR cc_start: 0.9208 (t80) cc_final: 0.8517 (t80) REVERT: D 493 TRP cc_start: 0.7518 (m100) cc_final: 0.6593 (m100) REVERT: D 512 ASP cc_start: 0.6539 (m-30) cc_final: 0.5917 (t0) REVERT: D 548 LEU cc_start: 0.9371 (pt) cc_final: 0.9141 (mt) REVERT: D 578 MET cc_start: 0.8735 (mtp) cc_final: 0.8296 (mtm) REVERT: D 589 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8314 (mmtt) REVERT: D 632 LEU cc_start: 0.9552 (mt) cc_final: 0.9250 (mt) REVERT: D 730 LEU cc_start: 0.9165 (pt) cc_final: 0.8959 (pt) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.1328 time to fit residues: 108.3024 Evaluate side-chains 376 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 561 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 301 HIS ** 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 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063743 restraints weight = 88154.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065118 restraints weight = 61693.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066189 restraints weight = 47721.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066812 restraints weight = 39518.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067432 restraints weight = 34663.837| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 21884 Z= 0.171 Angle : 0.753 8.898 29632 Z= 0.382 Chirality : 0.042 0.167 3384 Planarity : 0.004 0.066 3724 Dihedral : 5.977 36.806 2864 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.64 % Favored : 85.20 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.99 (0.16), residues: 2636 helix: 0.21 (0.13), residues: 1480 sheet: -3.91 (0.56), residues: 48 loop : -3.48 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.016 0.002 TYR C 359 PHE 0.038 0.001 PHE C 526 TRP 0.036 0.002 TRP D 742 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00371 (21884) covalent geometry : angle 0.75302 (29632) hydrogen bonds : bond 0.04249 ( 916) hydrogen bonds : angle 4.52276 ( 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 496 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.9001 (m-70) cc_final: 0.8404 (m90) REVERT: A 423 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7290 (mm-30) REVERT: A 448 TYR cc_start: 0.9258 (t80) cc_final: 0.8572 (t80) REVERT: A 493 TRP cc_start: 0.7320 (m100) cc_final: 0.6553 (m100) REVERT: A 512 ASP cc_start: 0.6683 (m-30) cc_final: 0.5964 (t0) REVERT: A 548 LEU cc_start: 0.9189 (pt) cc_final: 0.8847 (mm) REVERT: A 572 MET cc_start: 0.8983 (mmm) cc_final: 0.8645 (mmm) REVERT: A 574 MET cc_start: 0.8044 (ppp) cc_final: 0.7383 (ppp) REVERT: A 578 MET cc_start: 0.8729 (mtp) cc_final: 0.8221 (mtm) REVERT: A 594 TYR cc_start: 0.7583 (t80) cc_final: 0.7326 (t80) REVERT: A 735 ASN cc_start: 0.8019 (p0) cc_final: 0.7798 (p0) REVERT: B 141 ASP cc_start: 0.8978 (m-30) cc_final: 0.8657 (t0) REVERT: B 388 SER cc_start: 0.8332 (m) cc_final: 0.7548 (p) REVERT: B 401 ASN cc_start: 0.8103 (t0) cc_final: 0.7836 (t0) REVERT: B 423 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 448 TYR cc_start: 0.9077 (t80) cc_final: 0.8862 (t80) REVERT: B 453 ILE cc_start: 0.9185 (mm) cc_final: 0.8924 (tp) REVERT: B 484 LEU cc_start: 0.8798 (tp) cc_final: 0.8491 (pp) REVERT: B 493 TRP cc_start: 0.7859 (m100) cc_final: 0.6995 (m100) REVERT: B 574 MET cc_start: 0.7985 (ppp) cc_final: 0.7086 (ppp) REVERT: B 578 MET cc_start: 0.8826 (mtp) cc_final: 0.8247 (mtm) REVERT: B 735 ASN cc_start: 0.6672 (m110) cc_final: 0.6185 (m110) REVERT: C 141 ASP cc_start: 0.9161 (t0) cc_final: 0.8891 (t0) REVERT: C 292 GLN cc_start: 0.7579 (mp10) cc_final: 0.7223 (mp10) REVERT: C 336 MET cc_start: 0.7136 (tmm) cc_final: 0.6896 (tmm) REVERT: C 388 SER cc_start: 0.8227 (m) cc_final: 0.7417 (m) REVERT: C 418 GLU cc_start: 0.9113 (mp0) cc_final: 0.8789 (mp0) REVERT: C 453 ILE cc_start: 0.9188 (mm) cc_final: 0.8943 (tp) REVERT: C 455 LEU cc_start: 0.9507 (tp) cc_final: 0.9263 (tp) REVERT: C 488 MET cc_start: 0.8516 (ppp) cc_final: 0.8274 (ppp) REVERT: C 529 GLN cc_start: 0.9474 (tp40) cc_final: 0.9171 (tp40) REVERT: C 574 MET cc_start: 0.7949 (ppp) cc_final: 0.7116 (ppp) REVERT: C 578 MET cc_start: 0.8835 (mtp) cc_final: 0.8277 (mtp) REVERT: C 632 LEU cc_start: 0.9477 (mt) cc_final: 0.9209 (mm) REVERT: D 210 GLU cc_start: 0.9025 (tt0) cc_final: 0.8756 (tm-30) REVERT: D 323 MET cc_start: 0.8314 (tpt) cc_final: 0.8083 (tpt) REVERT: D 418 GLU cc_start: 0.8688 (mp0) cc_final: 0.8395 (mp0) REVERT: D 448 TYR cc_start: 0.9257 (t80) cc_final: 0.8538 (t80) REVERT: D 493 TRP cc_start: 0.7513 (m100) cc_final: 0.6762 (m100) REVERT: D 512 ASP cc_start: 0.6515 (m-30) cc_final: 0.5928 (t0) REVERT: D 548 LEU cc_start: 0.9315 (pt) cc_final: 0.9040 (mm) REVERT: D 578 MET cc_start: 0.8671 (mtp) cc_final: 0.8403 (mtm) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.1352 time to fit residues: 108.3332 Evaluate side-chains 373 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 7.9990 chunk 38 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 244 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 274 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 114 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 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 301 HIS ** 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 585 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065533 restraints weight = 86440.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067232 restraints weight = 58477.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068307 restraints weight = 43401.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069181 restraints weight = 35514.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069728 restraints weight = 30606.910| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21884 Z= 0.131 Angle : 0.741 9.045 29632 Z= 0.369 Chirality : 0.042 0.555 3384 Planarity : 0.004 0.071 3724 Dihedral : 5.660 34.904 2864 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.28 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -1.81 (0.17), residues: 2636 helix: 0.42 (0.13), residues: 1456 sheet: -3.99 (0.55), residues: 48 loop : -3.42 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 122 TYR 0.014 0.001 TYR A 409 PHE 0.033 0.001 PHE C 597 TRP 0.022 0.002 TRP D 742 HIS 0.004 0.000 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00277 (21884) covalent geometry : angle 0.74117 (29632) hydrogen bonds : bond 0.03975 ( 916) hydrogen bonds : angle 4.34298 ( 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 507 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 0.853 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: 0.8878 (t0) cc_final: 0.8562 (m110) REVERT: A 301 HIS cc_start: 0.9064 (m-70) cc_final: 0.8392 (m90) REVERT: A 318 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8577 (tppt) REVERT: A 448 TYR cc_start: 0.9317 (t80) cc_final: 0.8526 (t80) REVERT: A 484 LEU cc_start: 0.8749 (tp) cc_final: 0.8547 (mt) REVERT: A 488 MET cc_start: 0.8518 (ppp) cc_final: 0.8278 (ppp) REVERT: A 493 TRP cc_start: 0.7399 (m100) cc_final: 0.6704 (m100) REVERT: A 512 ASP cc_start: 0.6529 (m-30) cc_final: 0.5772 (t0) REVERT: A 548 LEU cc_start: 0.9197 (pt) cc_final: 0.8775 (mm) REVERT: A 553 LEU cc_start: 0.9553 (tt) cc_final: 0.9170 (pp) REVERT: A 574 MET cc_start: 0.8013 (ppp) cc_final: 0.7164 (ppp) REVERT: A 578 MET cc_start: 0.8874 (mtp) cc_final: 0.8214 (mtm) REVERT: A 687 GLU cc_start: 0.8621 (tt0) cc_final: 0.7993 (tm-30) REVERT: A 691 ILE cc_start: 0.9673 (mp) cc_final: 0.8541 (mp) REVERT: B 134 GLU cc_start: 0.8608 (pm20) cc_final: 0.8206 (pm20) REVERT: B 141 ASP cc_start: 0.9003 (m-30) cc_final: 0.8647 (t70) REVERT: B 423 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 448 TYR cc_start: 0.9137 (t80) cc_final: 0.8831 (t80) REVERT: B 453 ILE cc_start: 0.9113 (mm) cc_final: 0.8910 (tp) REVERT: B 484 LEU cc_start: 0.8769 (tp) cc_final: 0.8455 (pp) REVERT: B 548 LEU cc_start: 0.9329 (pt) cc_final: 0.9031 (mm) REVERT: B 574 MET cc_start: 0.8009 (ppp) cc_final: 0.7187 (ppp) REVERT: B 578 MET cc_start: 0.9021 (mtp) cc_final: 0.8427 (mtm) REVERT: B 594 TYR cc_start: 0.7851 (t80) cc_final: 0.7249 (t80) REVERT: B 735 ASN cc_start: 0.6673 (m110) cc_final: 0.6253 (m-40) REVERT: C 141 ASP cc_start: 0.9204 (t0) cc_final: 0.8940 (t0) REVERT: C 292 GLN cc_start: 0.7698 (mp10) cc_final: 0.7272 (mp10) REVERT: C 336 MET cc_start: 0.7738 (tmm) cc_final: 0.7478 (tmm) REVERT: C 388 SER cc_start: 0.8027 (m) cc_final: 0.7238 (m) REVERT: C 418 GLU cc_start: 0.9180 (mp0) cc_final: 0.8777 (mp0) REVERT: C 464 ARG cc_start: 0.6316 (mtt-85) cc_final: 0.5632 (ttt180) REVERT: C 526 PHE cc_start: 0.8318 (m-80) cc_final: 0.8037 (m-10) REVERT: C 529 GLN cc_start: 0.9415 (tp40) cc_final: 0.9095 (tp40) REVERT: C 550 CYS cc_start: 0.8621 (t) cc_final: 0.8405 (t) REVERT: C 574 MET cc_start: 0.8005 (ppp) cc_final: 0.6795 (ppp) REVERT: C 578 MET cc_start: 0.8980 (mtp) cc_final: 0.8391 (mtm) REVERT: C 632 LEU cc_start: 0.9491 (mt) cc_final: 0.9280 (mm) REVERT: D 210 GLU cc_start: 0.9034 (tt0) cc_final: 0.8218 (tm-30) REVERT: D 415 ASN cc_start: 0.8733 (p0) cc_final: 0.8491 (p0) REVERT: D 418 GLU cc_start: 0.8821 (mp0) cc_final: 0.8397 (mp0) REVERT: D 419 MET cc_start: 0.8615 (pmm) cc_final: 0.8375 (pmm) REVERT: D 448 TYR cc_start: 0.9358 (t80) cc_final: 0.8766 (t80) REVERT: D 484 LEU cc_start: 0.8756 (tp) cc_final: 0.8525 (pp) REVERT: D 512 ASP cc_start: 0.6594 (m-30) cc_final: 0.5894 (t0) REVERT: D 572 MET cc_start: 0.9036 (mmm) cc_final: 0.8772 (mmm) REVERT: D 578 MET cc_start: 0.8862 (mtp) cc_final: 0.8355 (mtm) REVERT: D 614 LYS cc_start: 0.6983 (tppt) cc_final: 0.6350 (ptpp) REVERT: D 733 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6867 (mmm160) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1223 time to fit residues: 101.8622 Evaluate side-chains 398 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 10.0000 chunk 211 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 301 HIS ** 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 561 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 301 HIS ** 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 = 0.3387 r_free = 0.3387 target = 0.079912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062841 restraints weight = 89372.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064519 restraints weight = 61171.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065670 restraints weight = 45847.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066536 restraints weight = 37177.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066914 restraints weight = 31897.944| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21884 Z= 0.190 Angle : 0.777 9.639 29632 Z= 0.392 Chirality : 0.044 0.731 3384 Planarity : 0.005 0.086 3724 Dihedral : 5.842 34.021 2864 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.72 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -1.85 (0.17), residues: 2636 helix: 0.31 (0.13), residues: 1460 sheet: -3.73 (0.59), residues: 48 loop : -3.35 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 118 TYR 0.017 0.002 TYR B 359 PHE 0.031 0.002 PHE C 597 TRP 0.022 0.003 TRP D 493 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00413 (21884) covalent geometry : angle 0.77749 (29632) hydrogen bonds : bond 0.04260 ( 916) hydrogen bonds : angle 4.55411 ( 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 452 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.656 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 284 ASN cc_start: 0.8942 (t0) cc_final: 0.8543 (m110) REVERT: A 301 HIS cc_start: 0.9036 (m-70) cc_final: 0.8330 (m90) REVERT: A 318 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8693 (tppt) REVERT: A 448 TYR cc_start: 0.9341 (t80) cc_final: 0.8732 (t80) REVERT: A 493 TRP cc_start: 0.7682 (m100) cc_final: 0.7027 (m100) REVERT: A 512 ASP cc_start: 0.6675 (m-30) cc_final: 0.5907 (t0) REVERT: A 548 LEU cc_start: 0.9195 (pt) cc_final: 0.8877 (mm) REVERT: A 578 MET cc_start: 0.8857 (mtp) cc_final: 0.8387 (mtm) REVERT: A 632 LEU cc_start: 0.9533 (mt) cc_final: 0.9257 (mt) REVERT: A 730 LEU cc_start: 0.9223 (pt) cc_final: 0.9018 (pt) REVERT: B 141 ASP cc_start: 0.9002 (m-30) cc_final: 0.8612 (t0) REVERT: B 388 SER cc_start: 0.8183 (m) cc_final: 0.7143 (p) REVERT: B 423 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 448 TYR cc_start: 0.9246 (t80) cc_final: 0.8926 (t80) REVERT: B 484 LEU cc_start: 0.8809 (tp) cc_final: 0.8497 (pp) REVERT: B 493 TRP cc_start: 0.8069 (m100) cc_final: 0.7143 (m100) REVERT: B 578 MET cc_start: 0.8870 (mtp) cc_final: 0.8419 (mtm) REVERT: B 598 LEU cc_start: 0.9428 (mt) cc_final: 0.9206 (mt) REVERT: B 735 ASN cc_start: 0.6989 (m110) cc_final: 0.6577 (m-40) REVERT: C 141 ASP cc_start: 0.9251 (t0) cc_final: 0.8970 (t0) REVERT: C 388 SER cc_start: 0.7971 (m) cc_final: 0.6957 (m) REVERT: C 418 GLU cc_start: 0.9082 (mp0) cc_final: 0.8673 (mp0) REVERT: C 455 LEU cc_start: 0.9515 (tp) cc_final: 0.9300 (tp) REVERT: C 526 PHE cc_start: 0.8531 (m-80) cc_final: 0.8279 (m-10) REVERT: C 529 GLN cc_start: 0.9530 (tp40) cc_final: 0.8948 (tp40) REVERT: C 557 LEU cc_start: 0.8892 (mm) cc_final: 0.8531 (tp) REVERT: C 574 MET cc_start: 0.8131 (ppp) cc_final: 0.6860 (ppp) REVERT: C 578 MET cc_start: 0.8945 (mtp) cc_final: 0.8343 (mtm) REVERT: C 632 LEU cc_start: 0.9543 (mt) cc_final: 0.9265 (mm) REVERT: C 730 LEU cc_start: 0.9046 (pt) cc_final: 0.8826 (pt) REVERT: D 173 MET cc_start: 0.8915 (ptm) cc_final: 0.8276 (ppp) REVERT: D 210 GLU cc_start: 0.9019 (tt0) cc_final: 0.8762 (tm-30) REVERT: D 318 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8640 (tppt) REVERT: D 323 MET cc_start: 0.8636 (tpt) cc_final: 0.8362 (tpt) REVERT: D 448 TYR cc_start: 0.9264 (t80) cc_final: 0.8912 (t80) REVERT: D 512 ASP cc_start: 0.6535 (m-30) cc_final: 0.5794 (t0) REVERT: D 572 MET cc_start: 0.9098 (mmm) cc_final: 0.8752 (mmm) REVERT: D 574 MET cc_start: 0.8142 (ppp) cc_final: 0.7227 (ppp) REVERT: D 578 MET cc_start: 0.8832 (mtp) cc_final: 0.8351 (mtm) REVERT: D 731 CYS cc_start: 0.8082 (m) cc_final: 0.7859 (m) REVERT: D 733 ARG cc_start: 0.7220 (mmm160) cc_final: 0.6833 (mmm160) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1248 time to fit residues: 93.0675 Evaluate side-chains 373 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 20.0000 chunk 14 optimal weight: 10.0000 chunk 141 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 239 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 200 optimal weight: 0.0060 chunk 144 optimal weight: 10.0000 overall best weight: 2.4398 ------------------------------------------------------------------------------- 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 301 HIS ** 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 561 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 301 HIS ** 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 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064356 restraints weight = 88259.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066033 restraints weight = 60416.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067217 restraints weight = 45485.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068110 restraints weight = 36641.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068619 restraints weight = 31395.637| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21884 Z= 0.145 Angle : 0.761 9.526 29632 Z= 0.377 Chirality : 0.042 0.464 3384 Planarity : 0.004 0.083 3724 Dihedral : 5.656 32.125 2864 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.58 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 0.42 (0.14), residues: 1448 sheet: -3.72 (0.60), residues: 48 loop : -3.37 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 118 TYR 0.031 0.001 TYR D 547 PHE 0.031 0.001 PHE C 597 TRP 0.020 0.002 TRP B 739 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00317 (21884) covalent geometry : angle 0.76069 (29632) hydrogen bonds : bond 0.04057 ( 916) hydrogen bonds : angle 4.46857 ( 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 471 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.618 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 284 ASN cc_start: 0.8927 (t0) cc_final: 0.8558 (m110) REVERT: A 301 HIS cc_start: 0.9096 (m-70) cc_final: 0.8071 (m90) REVERT: A 318 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8571 (tppt) REVERT: A 336 MET cc_start: 0.7441 (tmm) cc_final: 0.7163 (tmm) REVERT: A 448 TYR cc_start: 0.9338 (t80) cc_final: 0.8695 (t80) REVERT: A 488 MET cc_start: 0.8517 (ppp) cc_final: 0.8306 (ppp) REVERT: A 493 TRP cc_start: 0.7663 (m100) cc_final: 0.6846 (m100) REVERT: A 512 ASP cc_start: 0.6614 (m-30) cc_final: 0.5863 (t0) REVERT: A 548 LEU cc_start: 0.9187 (pt) cc_final: 0.8834 (mm) REVERT: A 578 MET cc_start: 0.8853 (mtp) cc_final: 0.8229 (mtm) REVERT: A 594 TYR cc_start: 0.7845 (t80) cc_final: 0.7527 (t80) REVERT: A 632 LEU cc_start: 0.9524 (mt) cc_final: 0.9236 (mt) REVERT: A 687 GLU cc_start: 0.8572 (tt0) cc_final: 0.8069 (tm-30) REVERT: A 691 ILE cc_start: 0.9668 (mp) cc_final: 0.8602 (mp) REVERT: A 730 LEU cc_start: 0.9216 (pt) cc_final: 0.9005 (pt) REVERT: B 141 ASP cc_start: 0.8979 (m-30) cc_final: 0.8629 (t70) REVERT: B 318 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8953 (mmmm) REVERT: B 323 MET cc_start: 0.8514 (tpt) cc_final: 0.8035 (tpt) REVERT: B 388 SER cc_start: 0.8044 (m) cc_final: 0.7529 (m) REVERT: B 418 GLU cc_start: 0.8989 (mp0) cc_final: 0.8771 (mp0) REVERT: B 423 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 448 TYR cc_start: 0.9260 (t80) cc_final: 0.8930 (t80) REVERT: B 484 LEU cc_start: 0.8783 (tp) cc_final: 0.8452 (pp) REVERT: B 493 TRP cc_start: 0.7972 (m100) cc_final: 0.7270 (m100) REVERT: B 578 MET cc_start: 0.8911 (mtp) cc_final: 0.8365 (mtm) REVERT: B 598 LEU cc_start: 0.9465 (mt) cc_final: 0.9190 (mt) REVERT: B 735 ASN cc_start: 0.6919 (m110) cc_final: 0.6464 (m-40) REVERT: C 141 ASP cc_start: 0.9240 (t0) cc_final: 0.8948 (t0) REVERT: C 388 SER cc_start: 0.7778 (m) cc_final: 0.6759 (m) REVERT: C 418 GLU cc_start: 0.9072 (mp0) cc_final: 0.8644 (mp0) REVERT: C 464 ARG cc_start: 0.6314 (mtt-85) cc_final: 0.5861 (ttm-80) REVERT: C 493 TRP cc_start: 0.7529 (m100) cc_final: 0.7040 (m100) REVERT: C 526 PHE cc_start: 0.8532 (m-80) cc_final: 0.8292 (m-10) REVERT: C 529 GLN cc_start: 0.9486 (tp40) cc_final: 0.9154 (tp40) REVERT: C 574 MET cc_start: 0.8088 (ppp) cc_final: 0.6767 (ppp) REVERT: C 578 MET cc_start: 0.9009 (mtp) cc_final: 0.8377 (mtm) REVERT: C 632 LEU cc_start: 0.9528 (mt) cc_final: 0.9282 (mm) REVERT: C 730 LEU cc_start: 0.8941 (pt) cc_final: 0.8733 (pt) REVERT: D 173 MET cc_start: 0.8819 (ptm) cc_final: 0.8152 (ppp) REVERT: D 318 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8562 (tppt) REVERT: D 323 MET cc_start: 0.8600 (tpt) cc_final: 0.8333 (tpp) REVERT: D 512 ASP cc_start: 0.6554 (m-30) cc_final: 0.5772 (t0) REVERT: D 572 MET cc_start: 0.9035 (mmm) cc_final: 0.8706 (mmm) REVERT: D 574 MET cc_start: 0.8132 (ppp) cc_final: 0.7296 (ppp) REVERT: D 578 MET cc_start: 0.8860 (mtp) cc_final: 0.8341 (mtm) REVERT: D 614 LYS cc_start: 0.7276 (tppt) cc_final: 0.6641 (ptpp) REVERT: D 733 ARG cc_start: 0.7309 (mmm160) cc_final: 0.6950 (mmm160) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1236 time to fit residues: 95.6674 Evaluate side-chains 384 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 477 HIS ** B 561 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 301 HIS ** 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 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 = 0.3391 r_free = 0.3391 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063286 restraints weight = 89515.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064897 restraints weight = 63210.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.065774 restraints weight = 48045.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066610 restraints weight = 40408.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067060 restraints weight = 35371.022| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6332 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= 0.181 Angle : 0.800 10.266 29632 Z= 0.399 Chirality : 0.043 0.372 3384 Planarity : 0.005 0.073 3724 Dihedral : 5.797 33.699 2864 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.91 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.82 (0.17), residues: 2636 helix: 0.38 (0.14), residues: 1452 sheet: -3.61 (0.61), residues: 48 loop : -3.37 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 118 TYR 0.018 0.002 TYR C 359 PHE 0.031 0.002 PHE C 597 TRP 0.030 0.003 TRP B 739 HIS 0.019 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00394 (21884) covalent geometry : angle 0.79981 (29632) hydrogen bonds : bond 0.04223 ( 916) hydrogen bonds : angle 4.57213 ( 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 452 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.095 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: A 173 MET cc_start: 0.8357 (ptt) cc_final: 0.7630 (ppp) REVERT: A 284 ASN cc_start: 0.8855 (t0) cc_final: 0.8530 (m110) REVERT: A 301 HIS cc_start: 0.9045 (m-70) cc_final: 0.8020 (m90) REVERT: A 318 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8618 (tppt) REVERT: A 419 MET cc_start: 0.8555 (pmm) cc_final: 0.8328 (pmm) REVERT: A 448 TYR cc_start: 0.9328 (t80) cc_final: 0.8774 (t80) REVERT: A 488 MET cc_start: 0.8517 (ppp) cc_final: 0.8262 (ppp) REVERT: A 493 TRP cc_start: 0.7611 (m100) cc_final: 0.6975 (m100) REVERT: A 548 LEU cc_start: 0.9198 (pt) cc_final: 0.8866 (mm) REVERT: A 578 MET cc_start: 0.8661 (mtp) cc_final: 0.8393 (mtm) REVERT: A 632 LEU cc_start: 0.9486 (mt) cc_final: 0.9206 (mt) REVERT: A 687 GLU cc_start: 0.8504 (tt0) cc_final: 0.8125 (tm-30) REVERT: A 691 ILE cc_start: 0.9627 (mp) cc_final: 0.8566 (mp) REVERT: B 141 ASP cc_start: 0.8973 (m-30) cc_final: 0.8646 (t0) REVERT: B 318 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8849 (tppp) REVERT: B 323 MET cc_start: 0.8348 (tpt) cc_final: 0.8042 (tpt) REVERT: B 380 TRP cc_start: 0.7511 (t-100) cc_final: 0.7184 (t-100) REVERT: B 388 SER cc_start: 0.8306 (m) cc_final: 0.7291 (p) REVERT: B 423 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 448 TYR cc_start: 0.9192 (t80) cc_final: 0.8914 (t80) REVERT: B 484 LEU cc_start: 0.8787 (tp) cc_final: 0.8446 (pp) REVERT: B 493 TRP cc_start: 0.7987 (m100) cc_final: 0.7116 (m100) REVERT: B 578 MET cc_start: 0.8712 (mtp) cc_final: 0.8492 (mtm) REVERT: B 598 LEU cc_start: 0.9515 (mt) cc_final: 0.9310 (mt) REVERT: B 735 ASN cc_start: 0.7083 (m110) cc_final: 0.6650 (m-40) REVERT: C 141 ASP cc_start: 0.9234 (t0) cc_final: 0.8951 (t0) REVERT: C 388 SER cc_start: 0.7895 (m) cc_final: 0.6774 (m) REVERT: C 418 GLU cc_start: 0.9001 (mp0) cc_final: 0.8656 (mp0) REVERT: C 464 ARG cc_start: 0.6383 (mtt-85) cc_final: 0.5917 (ttm-80) REVERT: C 529 GLN cc_start: 0.9502 (tp40) cc_final: 0.9158 (tp40) REVERT: C 555 MET cc_start: 0.8662 (tpp) cc_final: 0.8429 (tpp) REVERT: C 574 MET cc_start: 0.8025 (ppp) cc_final: 0.6633 (ppp) REVERT: C 578 MET cc_start: 0.8789 (mtp) cc_final: 0.8205 (mtm) REVERT: C 590 PHE cc_start: 0.9202 (t80) cc_final: 0.8967 (t80) REVERT: C 632 LEU cc_start: 0.9507 (mt) cc_final: 0.9233 (mm) REVERT: D 173 MET cc_start: 0.8665 (ptm) cc_final: 0.8280 (ppp) REVERT: D 373 LEU cc_start: 0.9435 (mt) cc_final: 0.8483 (mt) REVERT: D 512 ASP cc_start: 0.6633 (m-30) cc_final: 0.5900 (t0) REVERT: D 562 MET cc_start: 0.9395 (tpt) cc_final: 0.8868 (tpp) REVERT: D 572 MET cc_start: 0.9010 (mmm) cc_final: 0.8655 (mmm) REVERT: D 574 MET cc_start: 0.8028 (ppp) cc_final: 0.7092 (ppp) REVERT: D 578 MET cc_start: 0.8779 (mtp) cc_final: 0.8302 (mtm) REVERT: D 614 LYS cc_start: 0.7173 (tppt) cc_final: 0.6478 (ptpp) REVERT: D 733 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6839 (mmm160) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1318 time to fit residues: 97.4296 Evaluate side-chains 362 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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: 0.8980 chunk 67 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 259 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 235 optimal weight: 0.0060 chunk 66 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 561 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 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.083657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066742 restraints weight = 86997.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068287 restraints weight = 61233.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069506 restraints weight = 47007.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070218 restraints weight = 38242.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070882 restraints weight = 33311.876| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21884 Z= 0.133 Angle : 0.783 9.941 29632 Z= 0.380 Chirality : 0.042 0.334 3384 Planarity : 0.004 0.075 3724 Dihedral : 5.447 30.259 2864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.41 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.78 (0.17), residues: 2636 helix: 0.41 (0.13), residues: 1452 sheet: -3.73 (0.59), residues: 48 loop : -3.35 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 118 TYR 0.022 0.001 TYR C 540 PHE 0.022 0.001 PHE C 526 TRP 0.017 0.002 TRP D 742 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00277 (21884) covalent geometry : angle 0.78322 (29632) hydrogen bonds : bond 0.03861 ( 916) hydrogen bonds : angle 4.36376 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.86 seconds wall clock time: 56 minutes 50.42 seconds (3410.42 seconds total)