Starting phenix.real_space_refine on Fri Jun 5 06:36:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7s_7824/06_2026/6d7s_7824.map" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12280 2.51 5 N 3218 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19018 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4753 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Unresolved chain links: 2 Chain breaks: 1 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 4.58, per 1000 atoms: 0.24 Number of scatterers: 19018 At special positions: 0 Unit cell: (136.22, 136.22, 121.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3364 8.00 N 3218 7.00 C 12280 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: 1.51 Conformation dependent library (CDL) restraints added in 840.4 milliseconds 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 62.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.609A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.737A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 342 removed outlier: 3.556A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 346 No H-bonds generated for 'chain 'B' and resid 345 through 346' Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 4.381A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.609A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.683A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.567A pdb=" N PHE C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.345A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.579A pdb=" N ALA D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.562A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.929A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.537A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.288A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.566A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 587 removed outlier: 3.627A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA6, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.843A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2403 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: 3.38 Time building geometry restraints manager: 2.07 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: 6085 1.34 - 1.46: 4458 1.46 - 1.58: 8641 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 19448 Sorted by residual: bond pdb=" C GLU C 164 " pdb=" N HIS C 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.42e+00 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.34e+00 bond pdb=" C GLU B 164 " pdb=" N HIS B 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.32e+00 bond pdb=" C GLU D 164 " pdb=" N HIS D 165 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.27e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.83e+00 ... (remaining 19443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 26008 3.67 - 7.35: 310 7.35 - 11.02: 64 11.02 - 14.70: 0 14.70 - 18.37: 4 Bond angle restraints: 26386 Sorted by residual: angle pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta sigma weight residual 120.54 129.35 -8.81 1.35e+00 5.49e-01 4.26e+01 angle pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta sigma weight residual 120.54 129.33 -8.79 1.35e+00 5.49e-01 4.24e+01 angle pdb=" C ASP C 223 " pdb=" N ARG C 224 " pdb=" CA ARG C 224 " ideal model delta sigma weight residual 120.54 129.31 -8.77 1.35e+00 5.49e-01 4.22e+01 angle pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta sigma weight residual 120.54 129.29 -8.75 1.35e+00 5.49e-01 4.20e+01 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 114.56 106.46 8.10 1.27e+00 6.20e-01 4.06e+01 ... (remaining 26381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10916 16.66 - 33.33: 584 33.33 - 49.99: 132 49.99 - 66.66: 8 66.66 - 83.32: 28 Dihedral angle restraints: 11668 sinusoidal: 4718 harmonic: 6950 Sorted by residual: dihedral pdb=" CA SER B 291 " pdb=" C SER B 291 " pdb=" N LEU B 292 " pdb=" CA LEU B 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 291 " pdb=" C SER A 291 " pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER D 291 " pdb=" C SER D 291 " pdb=" N LEU D 292 " pdb=" CA LEU D 292 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 11665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2189 0.057 - 0.114: 703 0.114 - 0.171: 94 0.171 - 0.228: 20 0.228 - 0.285: 4 Chirality restraints: 3010 Sorted by residual: chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3007 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 354 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " -0.036 5.00e-02 4.00e+02 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4620 2.78 - 3.31: 18427 3.31 - 3.84: 30816 3.84 - 4.37: 36892 4.37 - 4.90: 58694 Nonbonded interactions: 149449 Sorted by model distance: nonbonded pdb=" OD2 ASP B 279 " pdb=" OG1 THR B 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP C 279 " pdb=" OG1 THR C 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP A 279 " pdb=" OG1 THR A 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP D 279 " pdb=" OG1 THR D 281 " model vdw 2.249 3.040 nonbonded pdb=" O ARG B 443 " pdb=" OG SER B 446 " model vdw 2.295 3.040 ... (remaining 149444 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 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = (chain 'D' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.890 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.007 0.077 19448 Z= 0.338 Angle : 1.160 18.370 26386 Z= 0.640 Chirality : 0.056 0.285 3010 Planarity : 0.007 0.064 3330 Dihedral : 11.857 83.321 7168 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.07 % Favored : 87.76 % Rotamer: Outliers : 1.17 % Allowed : 2.33 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.61 (0.12), residues: 2353 helix: -3.58 (0.08), residues: 1298 sheet: -5.34 (0.26), residues: 40 loop : -3.75 (0.16), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 385 TYR 0.021 0.003 TYR A 524 PHE 0.034 0.003 PHE D 162 TRP 0.022 0.003 TRP B 593 HIS 0.018 0.003 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.34 (19448) covalent geometry : angle 1.16046 / 0.64 (26386) hydrogen bonds : bond 0.29838 / 19.71 ( 833) hydrogen bonds : angle 9.05244 / 6.32 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 717 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 63 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8093 (tptp) REVERT: A 92 LEU cc_start: 0.8365 (tp) cc_final: 0.7542 (tt) REVERT: A 200 LEU cc_start: 0.9531 (mt) cc_final: 0.9278 (mt) REVERT: A 245 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8927 (tttt) REVERT: A 294 GLU cc_start: 0.8950 (tt0) cc_final: 0.8399 (pt0) REVERT: A 464 ASN cc_start: 0.8532 (t160) cc_final: 0.8216 (t160) REVERT: A 466 MET cc_start: 0.9212 (mmt) cc_final: 0.8843 (mmm) REVERT: A 475 LEU cc_start: 0.8907 (mp) cc_final: 0.8321 (tt) REVERT: A 485 MET cc_start: 0.9056 (mmp) cc_final: 0.8580 (mmp) REVERT: A 491 MET cc_start: 0.7738 (mmm) cc_final: 0.6912 (tpt) REVERT: A 578 MET cc_start: 0.9095 (mmt) cc_final: 0.8841 (mmt) REVERT: A 580 ASP cc_start: 0.9070 (t0) cc_final: 0.8672 (t0) REVERT: A 590 ASP cc_start: 0.8144 (p0) cc_final: 0.7928 (p0) REVERT: A 591 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8633 (mp0) REVERT: B 36 GLN cc_start: 0.7605 (tm130) cc_final: 0.7243 (tm-30) REVERT: B 63 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8154 (tptp) REVERT: B 92 LEU cc_start: 0.8353 (tp) cc_final: 0.6467 (tt) REVERT: B 245 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8889 (mttt) REVERT: B 280 LEU cc_start: 0.8969 (tp) cc_final: 0.8671 (tp) REVERT: B 389 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7267 (tp30) REVERT: B 455 SER cc_start: 0.9351 (m) cc_final: 0.9125 (p) REVERT: B 463 CYS cc_start: 0.8989 (m) cc_final: 0.8462 (t) REVERT: B 491 MET cc_start: 0.7778 (mmm) cc_final: 0.7123 (tpt) REVERT: B 508 PHE cc_start: 0.9134 (m-10) cc_final: 0.8724 (m-80) REVERT: B 520 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8657 (tp) REVERT: B 535 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 580 ASP cc_start: 0.8811 (t0) cc_final: 0.8609 (t0) REVERT: C 63 LYS cc_start: 0.8538 (ttpp) cc_final: 0.7677 (tptp) REVERT: C 92 LEU cc_start: 0.8599 (tp) cc_final: 0.8279 (pt) REVERT: C 130 MET cc_start: 0.6892 (tpp) cc_final: 0.6469 (tpp) REVERT: C 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8201 (pt) REVERT: C 209 LYS cc_start: 0.8453 (mttp) cc_final: 0.8078 (ptpt) REVERT: C 245 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8508 (tttt) REVERT: C 400 LEU cc_start: 0.9075 (mt) cc_final: 0.8365 (tt) REVERT: C 464 ASN cc_start: 0.8694 (t160) cc_final: 0.8388 (t0) REVERT: C 466 MET cc_start: 0.8944 (mmt) cc_final: 0.8512 (mmm) REVERT: C 485 MET cc_start: 0.8937 (mmp) cc_final: 0.8143 (mmp) REVERT: C 512 PHE cc_start: 0.8804 (m-10) cc_final: 0.8596 (m-80) REVERT: C 515 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7782 (tp30) REVERT: C 559 TYR cc_start: 0.8959 (t80) cc_final: 0.8607 (t80) REVERT: C 607 LYS cc_start: 0.8838 (mttp) cc_final: 0.8278 (mmmt) REVERT: D 63 LYS cc_start: 0.8510 (ttpp) cc_final: 0.7706 (tptp) REVERT: D 92 LEU cc_start: 0.8513 (tp) cc_final: 0.6826 (tt) REVERT: D 309 ASP cc_start: 0.8664 (m-30) cc_final: 0.8233 (m-30) REVERT: D 466 MET cc_start: 0.9266 (mmt) cc_final: 0.8621 (mmm) REVERT: D 485 MET cc_start: 0.8903 (mmp) cc_final: 0.8485 (mmp) REVERT: D 491 MET cc_start: 0.7280 (mmm) cc_final: 0.6857 (tpp) REVERT: D 591 GLU cc_start: 0.8943 (mt-10) cc_final: 0.7984 (mm-30) outliers start: 24 outliers final: 8 residues processed: 739 average time/residue: 0.1370 time to fit residues: 154.5831 Evaluate side-chains 451 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 441 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 217 ASN A 267 GLN A 483 GLN A 596 GLN B 73 HIS B 165 HIS B 217 ASN B 267 GLN B 426 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 165 HIS C 217 ASN C 257 GLN C 267 GLN C 357 ASN C 548 ASN D 73 HIS D 118 GLN D 165 HIS D 217 ASN D 267 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073547 restraints weight = 65787.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075540 restraints weight = 38296.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076930 restraints weight = 25946.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077926 restraints weight = 19539.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078559 restraints weight = 15874.426| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19448 Z= 0.170 Angle : 0.779 13.325 26386 Z= 0.396 Chirality : 0.044 0.185 3010 Planarity : 0.005 0.055 3330 Dihedral : 6.413 28.206 2590 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.53 % Allowed : 3.55 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.15), residues: 2353 helix: -1.25 (0.13), residues: 1313 sheet: -5.24 (0.17), residues: 56 loop : -3.31 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 224 TYR 0.015 0.001 TYR B 559 PHE 0.028 0.002 PHE B 523 TRP 0.017 0.001 TRP B 29 HIS 0.007 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (19448) covalent geometry : angle 0.77885 / 0.40 (26386) hydrogen bonds : bond 0.04407 / 2.98 ( 833) hydrogen bonds : angle 5.01621 / 3.45 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 551 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8158 (tptp) REVERT: A 65 LEU cc_start: 0.8308 (mp) cc_final: 0.8013 (mp) REVERT: A 78 MET cc_start: 0.4675 (ptt) cc_final: 0.4247 (ptt) REVERT: A 92 LEU cc_start: 0.8251 (tp) cc_final: 0.7737 (tt) REVERT: A 215 MET cc_start: 0.8400 (mpp) cc_final: 0.7685 (mpp) REVERT: A 245 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8812 (tttt) REVERT: A 294 GLU cc_start: 0.8500 (tt0) cc_final: 0.8283 (pt0) REVERT: A 330 CYS cc_start: 0.9083 (m) cc_final: 0.8814 (m) REVERT: A 339 TYR cc_start: 0.9138 (t80) cc_final: 0.8611 (t80) REVERT: A 464 ASN cc_start: 0.8423 (t0) cc_final: 0.8175 (t0) REVERT: A 466 MET cc_start: 0.9186 (mmt) cc_final: 0.8985 (mmm) REVERT: A 485 MET cc_start: 0.9300 (mmp) cc_final: 0.8551 (mmp) REVERT: A 493 PHE cc_start: 0.8881 (t80) cc_final: 0.8644 (t80) REVERT: A 578 MET cc_start: 0.9282 (mmt) cc_final: 0.8848 (mmt) REVERT: A 580 ASP cc_start: 0.9361 (t0) cc_final: 0.9060 (t0) REVERT: B 63 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8236 (tptp) REVERT: B 65 LEU cc_start: 0.8240 (mp) cc_final: 0.7984 (mp) REVERT: B 92 LEU cc_start: 0.8342 (tp) cc_final: 0.7491 (tt) REVERT: B 127 ASN cc_start: 0.8454 (m110) cc_final: 0.7296 (p0) REVERT: B 245 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8703 (mttt) REVERT: B 389 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7451 (tp30) REVERT: B 455 SER cc_start: 0.9223 (m) cc_final: 0.8937 (p) REVERT: B 464 ASN cc_start: 0.8533 (t0) cc_final: 0.8256 (t0) REVERT: B 474 MET cc_start: 0.7169 (ptt) cc_final: 0.6682 (ptt) REVERT: B 478 PHE cc_start: 0.8580 (m-80) cc_final: 0.8285 (m-10) REVERT: B 481 MET cc_start: 0.8572 (mtp) cc_final: 0.8252 (mtm) REVERT: B 491 MET cc_start: 0.7988 (mmm) cc_final: 0.7290 (tpt) REVERT: B 535 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7210 (mt-10) REVERT: C 63 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7819 (tptp) REVERT: C 67 TYR cc_start: 0.8376 (m-10) cc_final: 0.8151 (m-80) REVERT: C 110 MET cc_start: 0.8338 (mmm) cc_final: 0.8133 (mmm) REVERT: C 215 MET cc_start: 0.8321 (mpp) cc_final: 0.8056 (mpp) REVERT: C 232 LEU cc_start: 0.8794 (tp) cc_final: 0.8518 (tp) REVERT: C 245 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8436 (mttt) REVERT: C 400 LEU cc_start: 0.9193 (mt) cc_final: 0.8502 (tt) REVERT: C 428 LEU cc_start: 0.9481 (mp) cc_final: 0.9251 (mm) REVERT: C 464 ASN cc_start: 0.8853 (t0) cc_final: 0.8246 (t0) REVERT: C 466 MET cc_start: 0.9274 (mmt) cc_final: 0.8857 (mmm) REVERT: C 474 MET cc_start: 0.7322 (ptt) cc_final: 0.6384 (ptt) REVERT: C 475 LEU cc_start: 0.9161 (tp) cc_final: 0.8681 (tp) REVERT: C 485 MET cc_start: 0.9031 (mmp) cc_final: 0.8569 (mmp) REVERT: C 559 TYR cc_start: 0.9153 (t80) cc_final: 0.8501 (t80) REVERT: C 578 MET cc_start: 0.8663 (mmm) cc_final: 0.8434 (mmm) REVERT: C 591 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8098 (tm-30) REVERT: D 63 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7905 (tptp) REVERT: D 65 LEU cc_start: 0.8364 (mp) cc_final: 0.8145 (mp) REVERT: D 78 MET cc_start: 0.5099 (ptt) cc_final: 0.4685 (ptt) REVERT: D 92 LEU cc_start: 0.8387 (tp) cc_final: 0.8038 (tt) REVERT: D 181 LEU cc_start: 0.9283 (mm) cc_final: 0.9077 (tp) REVERT: D 245 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8910 (tttt) REVERT: D 307 ILE cc_start: 0.9541 (mm) cc_final: 0.9322 (mm) REVERT: D 339 TYR cc_start: 0.9077 (t80) cc_final: 0.8669 (t80) REVERT: D 435 MET cc_start: 0.9237 (mmp) cc_final: 0.8921 (mmp) REVERT: D 442 MET cc_start: 0.8378 (ttm) cc_final: 0.8177 (ttm) REVERT: D 454 MET cc_start: 0.8808 (tpp) cc_final: 0.8598 (tpp) REVERT: D 492 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7795 (ptm160) REVERT: D 591 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8502 (mt-10) outliers start: 11 outliers final: 3 residues processed: 557 average time/residue: 0.1238 time to fit residues: 109.1380 Evaluate side-chains 393 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 154 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 206 GLN A 290 GLN B 206 GLN B 464 ASN B 546 ASN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN D 290 GLN D 572 ASN D 582 HIS D 596 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070826 restraints weight = 66853.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.072753 restraints weight = 38437.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074061 restraints weight = 25883.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074953 restraints weight = 19455.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075632 restraints weight = 15824.467| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19448 Z= 0.196 Angle : 0.761 13.300 26386 Z= 0.386 Chirality : 0.044 0.197 3010 Planarity : 0.005 0.042 3330 Dihedral : 6.038 25.029 2590 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.16), residues: 2353 helix: -0.25 (0.14), residues: 1326 sheet: -5.08 (0.20), residues: 56 loop : -3.23 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 363 TYR 0.016 0.001 TYR B 559 PHE 0.025 0.002 PHE D 523 TRP 0.012 0.001 TRP B 321 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (19448) covalent geometry : angle 0.76102 / 0.39 (26386) hydrogen bonds : bond 0.03865 / 2.62 ( 833) hydrogen bonds : angle 4.70085 / 3.24 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 477 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8136 (tptp) REVERT: A 66 LYS cc_start: 0.7903 (mppt) cc_final: 0.7529 (pptt) REVERT: A 209 LYS cc_start: 0.8714 (mttt) cc_final: 0.8496 (mttt) REVERT: A 245 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8637 (tttt) REVERT: A 330 CYS cc_start: 0.9197 (m) cc_final: 0.8915 (m) REVERT: A 339 TYR cc_start: 0.9077 (t80) cc_final: 0.8628 (t80) REVERT: A 463 CYS cc_start: 0.9009 (m) cc_final: 0.8573 (t) REVERT: A 464 ASN cc_start: 0.8714 (t0) cc_final: 0.8088 (t0) REVERT: A 466 MET cc_start: 0.9193 (mmt) cc_final: 0.8973 (mmm) REVERT: A 485 MET cc_start: 0.9296 (mmp) cc_final: 0.8403 (mmp) REVERT: A 501 ILE cc_start: 0.9548 (mm) cc_final: 0.9278 (tp) REVERT: A 506 SER cc_start: 0.9700 (m) cc_final: 0.9313 (p) REVERT: A 580 ASP cc_start: 0.9222 (t0) cc_final: 0.8967 (t0) REVERT: B 29 TRP cc_start: 0.7543 (p90) cc_final: 0.7240 (p90) REVERT: B 63 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8198 (tptp) REVERT: B 66 LYS cc_start: 0.7834 (mppt) cc_final: 0.7426 (pptt) REVERT: B 78 MET cc_start: 0.5194 (ptt) cc_final: 0.4985 (ptt) REVERT: B 92 LEU cc_start: 0.8488 (tp) cc_final: 0.7911 (tt) REVERT: B 232 LEU cc_start: 0.8930 (tp) cc_final: 0.8683 (tp) REVERT: B 245 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8741 (mttt) REVERT: B 389 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7616 (tp30) REVERT: B 464 ASN cc_start: 0.8768 (t0) cc_final: 0.8459 (t0) REVERT: B 475 LEU cc_start: 0.9083 (mp) cc_final: 0.8762 (tp) REVERT: B 491 MET cc_start: 0.7881 (mmm) cc_final: 0.7315 (tpt) REVERT: B 535 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7257 (mt-10) REVERT: C 63 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7829 (tptp) REVERT: C 78 MET cc_start: 0.5546 (ptt) cc_final: 0.5318 (ptt) REVERT: C 215 MET cc_start: 0.8343 (mpp) cc_final: 0.8095 (mpp) REVERT: C 245 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8492 (mttt) REVERT: C 330 CYS cc_start: 0.9141 (m) cc_final: 0.8923 (m) REVERT: C 428 LEU cc_start: 0.9553 (mp) cc_final: 0.9066 (mm) REVERT: C 464 ASN cc_start: 0.9027 (t0) cc_final: 0.8464 (t0) REVERT: C 466 MET cc_start: 0.9396 (mmt) cc_final: 0.9038 (mmm) REVERT: C 491 MET cc_start: 0.8083 (tpt) cc_final: 0.7827 (tpp) REVERT: C 522 HIS cc_start: 0.8632 (m-70) cc_final: 0.8342 (m-70) REVERT: C 559 TYR cc_start: 0.9281 (t80) cc_final: 0.8754 (t80) REVERT: C 591 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8223 (tm-30) REVERT: C 592 LEU cc_start: 0.9515 (mm) cc_final: 0.8761 (mm) REVERT: D 63 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7973 (tptp) REVERT: D 78 MET cc_start: 0.4976 (ptt) cc_final: 0.4597 (ptt) REVERT: D 99 MET cc_start: 0.8781 (mmm) cc_final: 0.8397 (mmm) REVERT: D 181 LEU cc_start: 0.9318 (mm) cc_final: 0.9110 (tp) REVERT: D 245 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8871 (tttt) REVERT: D 339 TYR cc_start: 0.8990 (t80) cc_final: 0.8527 (t80) REVERT: D 454 MET cc_start: 0.8978 (tpp) cc_final: 0.8717 (tpp) REVERT: D 463 CYS cc_start: 0.9068 (m) cc_final: 0.8255 (t) REVERT: D 466 MET cc_start: 0.9111 (tpp) cc_final: 0.7535 (mpp) REVERT: D 485 MET cc_start: 0.8982 (mmp) cc_final: 0.8389 (mmp) REVERT: D 559 TYR cc_start: 0.9423 (t80) cc_final: 0.9087 (t80) REVERT: D 577 MET cc_start: 0.9262 (tpp) cc_final: 0.8796 (tpp) REVERT: D 590 ASP cc_start: 0.8114 (p0) cc_final: 0.7610 (p0) REVERT: D 591 GLU cc_start: 0.8756 (mt-10) cc_final: 0.7782 (mm-30) outliers start: 4 outliers final: 0 residues processed: 481 average time/residue: 0.1264 time to fit residues: 96.5210 Evaluate side-chains 359 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 149 optimal weight: 0.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A 596 GLN B 290 GLN B 464 ASN C 197 ASN C 290 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073697 restraints weight = 65973.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075695 restraints weight = 37994.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077112 restraints weight = 25652.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078104 restraints weight = 19196.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078783 restraints weight = 15524.215| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19448 Z= 0.130 Angle : 0.700 13.572 26386 Z= 0.347 Chirality : 0.042 0.189 3010 Planarity : 0.004 0.041 3330 Dihedral : 5.669 25.140 2590 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.24 % Allowed : 3.30 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.17), residues: 2353 helix: 0.19 (0.14), residues: 1321 sheet: -4.75 (0.25), residues: 56 loop : -3.24 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 606 TYR 0.012 0.001 TYR B 559 PHE 0.031 0.002 PHE D 434 TRP 0.015 0.001 TRP C 29 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19448) covalent geometry : angle 0.69998 / 0.35 (26386) hydrogen bonds : bond 0.03303 / 2.22 ( 833) hydrogen bonds : angle 4.40042 / 3.02 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 477 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8251 (tptp) REVERT: A 110 MET cc_start: 0.8577 (mmm) cc_final: 0.8149 (mmm) REVERT: A 245 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8695 (tttt) REVERT: A 339 TYR cc_start: 0.9122 (t80) cc_final: 0.8611 (t80) REVERT: A 485 MET cc_start: 0.9193 (mmt) cc_final: 0.8442 (mmp) REVERT: A 506 SER cc_start: 0.9667 (m) cc_final: 0.9306 (p) REVERT: A 535 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 541 ILE cc_start: 0.9562 (mm) cc_final: 0.9347 (mm) REVERT: A 580 ASP cc_start: 0.9176 (t0) cc_final: 0.8934 (t0) REVERT: A 588 GLU cc_start: 0.7093 (mp0) cc_final: 0.6405 (mp0) REVERT: A 590 ASP cc_start: 0.7855 (p0) cc_final: 0.7462 (p0) REVERT: A 591 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8358 (mp0) REVERT: B 29 TRP cc_start: 0.7528 (p90) cc_final: 0.7267 (p90) REVERT: B 63 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8303 (tptp) REVERT: B 78 MET cc_start: 0.5134 (ptt) cc_final: 0.4915 (ptt) REVERT: B 336 TYR cc_start: 0.9511 (t80) cc_final: 0.9290 (t80) REVERT: B 389 GLU cc_start: 0.8817 (mt-10) cc_final: 0.7699 (tp30) REVERT: B 464 ASN cc_start: 0.8927 (t0) cc_final: 0.8496 (t0) REVERT: B 466 MET cc_start: 0.9121 (mmm) cc_final: 0.8899 (mmm) REVERT: B 491 MET cc_start: 0.8022 (mmm) cc_final: 0.7744 (tpt) REVERT: B 535 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7302 (mt-10) REVERT: B 577 MET cc_start: 0.8304 (ttm) cc_final: 0.7456 (ttm) REVERT: C 29 TRP cc_start: 0.7663 (p90) cc_final: 0.7424 (p90) REVERT: C 63 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8002 (tptp) REVERT: C 215 MET cc_start: 0.8327 (mpp) cc_final: 0.8076 (mpp) REVERT: C 232 LEU cc_start: 0.8807 (tp) cc_final: 0.8596 (tp) REVERT: C 245 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8497 (mttt) REVERT: C 330 CYS cc_start: 0.9066 (m) cc_final: 0.8011 (p) REVERT: C 331 MET cc_start: 0.8148 (mtm) cc_final: 0.6348 (mmt) REVERT: C 428 LEU cc_start: 0.9354 (mp) cc_final: 0.9097 (mm) REVERT: C 464 ASN cc_start: 0.8994 (t0) cc_final: 0.8440 (t0) REVERT: C 466 MET cc_start: 0.9417 (mmt) cc_final: 0.9163 (mmm) REVERT: C 485 MET cc_start: 0.9052 (mmp) cc_final: 0.8262 (mmp) REVERT: C 491 MET cc_start: 0.8195 (tpt) cc_final: 0.7812 (tpp) REVERT: C 559 TYR cc_start: 0.9316 (t80) cc_final: 0.8938 (t80) REVERT: C 578 MET cc_start: 0.8778 (mmm) cc_final: 0.8029 (mmm) REVERT: C 591 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8143 (tm-30) REVERT: C 592 LEU cc_start: 0.9547 (mm) cc_final: 0.8889 (mm) REVERT: D 63 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7919 (tptp) REVERT: D 245 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8876 (mttt) REVERT: D 339 TYR cc_start: 0.9048 (t80) cc_final: 0.8715 (t80) REVERT: D 464 ASN cc_start: 0.8981 (t0) cc_final: 0.8263 (t0) REVERT: D 485 MET cc_start: 0.8954 (mmp) cc_final: 0.8533 (mmp) REVERT: D 559 TYR cc_start: 0.9498 (t80) cc_final: 0.8877 (t80) REVERT: D 569 LEU cc_start: 0.9326 (tt) cc_final: 0.9119 (tt) REVERT: D 588 GLU cc_start: 0.7060 (mp0) cc_final: 0.6840 (mp0) REVERT: D 590 ASP cc_start: 0.7878 (p0) cc_final: 0.7476 (p0) REVERT: D 591 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7653 (mm-30) outliers start: 5 outliers final: 1 residues processed: 481 average time/residue: 0.1284 time to fit residues: 97.2186 Evaluate side-chains 360 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN B 464 ASN B 582 HIS C 118 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN C 582 HIS ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073362 restraints weight = 65169.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075381 restraints weight = 38076.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076753 restraints weight = 25933.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077728 restraints weight = 19665.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078411 restraints weight = 16028.408| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19448 Z= 0.129 Angle : 0.714 14.023 26386 Z= 0.350 Chirality : 0.043 0.297 3010 Planarity : 0.004 0.061 3330 Dihedral : 5.479 26.257 2590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 2353 helix: 0.33 (0.14), residues: 1327 sheet: -4.47 (0.29), residues: 56 loop : -3.18 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 606 TYR 0.013 0.001 TYR B 339 PHE 0.042 0.002 PHE A 456 TRP 0.012 0.001 TRP A 613 HIS 0.008 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (19448) covalent geometry : angle 0.71411 / 0.35 (26386) hydrogen bonds : bond 0.03185 / 2.14 ( 833) hydrogen bonds : angle 4.31602 / 2.95 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 0.715 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8183 (tptp) REVERT: A 66 LYS cc_start: 0.7982 (mppt) cc_final: 0.7514 (pptt) REVERT: A 245 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8711 (mttt) REVERT: A 339 TYR cc_start: 0.9095 (t80) cc_final: 0.8632 (t80) REVERT: A 464 ASN cc_start: 0.8621 (t160) cc_final: 0.8396 (t0) REVERT: A 466 MET cc_start: 0.9270 (tpp) cc_final: 0.8735 (mmm) REVERT: A 485 MET cc_start: 0.9043 (mmp) cc_final: 0.8547 (mmp) REVERT: A 506 SER cc_start: 0.9617 (m) cc_final: 0.9240 (p) REVERT: A 535 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 587 HIS cc_start: 0.7730 (t70) cc_final: 0.7181 (m-70) REVERT: A 588 GLU cc_start: 0.7055 (mp0) cc_final: 0.6316 (mp0) REVERT: A 590 ASP cc_start: 0.7735 (p0) cc_final: 0.7424 (p0) REVERT: A 591 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8287 (mp0) REVERT: B 29 TRP cc_start: 0.7570 (p90) cc_final: 0.7266 (p90) REVERT: B 63 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8312 (tptp) REVERT: B 78 MET cc_start: 0.5141 (ptt) cc_final: 0.4895 (ptt) REVERT: B 245 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8811 (mttt) REVERT: B 389 GLU cc_start: 0.8822 (mt-10) cc_final: 0.7695 (tp30) REVERT: B 454 MET cc_start: 0.8807 (mmm) cc_final: 0.8502 (tpt) REVERT: B 464 ASN cc_start: 0.8833 (t0) cc_final: 0.8428 (t0) REVERT: B 491 MET cc_start: 0.7911 (mmm) cc_final: 0.7672 (tpt) REVERT: B 506 SER cc_start: 0.9620 (m) cc_final: 0.9210 (p) REVERT: B 535 GLU cc_start: 0.8365 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 602 VAL cc_start: 0.9336 (t) cc_final: 0.9061 (p) REVERT: C 29 TRP cc_start: 0.7637 (p90) cc_final: 0.7409 (p90) REVERT: C 63 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8097 (tptp) REVERT: C 245 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8505 (mttt) REVERT: C 330 CYS cc_start: 0.9039 (m) cc_final: 0.7924 (p) REVERT: C 331 MET cc_start: 0.7956 (mtm) cc_final: 0.6258 (mmt) REVERT: C 464 ASN cc_start: 0.8931 (t0) cc_final: 0.8368 (t0) REVERT: C 466 MET cc_start: 0.9333 (mmt) cc_final: 0.9127 (mmm) REVERT: C 485 MET cc_start: 0.8990 (mmp) cc_final: 0.8325 (mmp) REVERT: C 489 ASP cc_start: 0.7974 (t0) cc_final: 0.6422 (t0) REVERT: C 491 MET cc_start: 0.7982 (tpt) cc_final: 0.7634 (tpp) REVERT: C 559 TYR cc_start: 0.9255 (t80) cc_final: 0.8729 (t80) REVERT: C 578 MET cc_start: 0.8664 (mmm) cc_final: 0.8063 (mmt) REVERT: C 589 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8319 (ttp80) REVERT: C 591 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8059 (tm-30) REVERT: C 592 LEU cc_start: 0.9517 (mm) cc_final: 0.8873 (mm) REVERT: D 63 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7922 (tptp) REVERT: D 110 MET cc_start: 0.8261 (mmm) cc_final: 0.7955 (mmm) REVERT: D 245 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8828 (tttt) REVERT: D 339 TYR cc_start: 0.9051 (t80) cc_final: 0.8716 (t80) REVERT: D 454 MET cc_start: 0.8809 (tpp) cc_final: 0.8480 (tpp) REVERT: D 464 ASN cc_start: 0.8943 (t0) cc_final: 0.8563 (t0) REVERT: D 485 MET cc_start: 0.9064 (mmp) cc_final: 0.8445 (mmp) REVERT: D 559 TYR cc_start: 0.9421 (t80) cc_final: 0.8666 (t80) REVERT: D 588 GLU cc_start: 0.6876 (mp0) cc_final: 0.6668 (mp0) REVERT: D 590 ASP cc_start: 0.7724 (p0) cc_final: 0.7378 (p0) REVERT: D 591 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7540 (mm-30) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.1342 time to fit residues: 99.8680 Evaluate side-chains 364 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 42 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 513 GLN B 582 HIS B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071924 restraints weight = 66815.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073859 restraints weight = 39304.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075244 restraints weight = 26916.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076212 restraints weight = 20294.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076910 restraints weight = 16483.753| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19448 Z= 0.189 Angle : 0.754 14.833 26386 Z= 0.374 Chirality : 0.044 0.210 3010 Planarity : 0.004 0.068 3330 Dihedral : 5.527 27.219 2590 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.20 % Favored : 89.76 % Rotamer: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.51 (0.17), residues: 2353 helix: 0.49 (0.14), residues: 1332 sheet: -4.08 (0.29), residues: 56 loop : -3.09 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 606 TYR 0.016 0.001 TYR B 559 PHE 0.038 0.002 PHE A 456 TRP 0.013 0.001 TRP B 495 HIS 0.008 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (19448) covalent geometry : angle 0.75426 / 0.37 (26386) hydrogen bonds : bond 0.03320 / 2.24 ( 833) hydrogen bonds : angle 4.40095 / 3.03 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 445 time to evaluate : 0.769 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8282 (tptp) REVERT: A 339 TYR cc_start: 0.9058 (t80) cc_final: 0.8703 (t80) REVERT: A 485 MET cc_start: 0.9120 (mmp) cc_final: 0.8272 (mmp) REVERT: A 535 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 578 MET cc_start: 0.9129 (mmt) cc_final: 0.8580 (mmt) REVERT: A 588 GLU cc_start: 0.7158 (mp0) cc_final: 0.6208 (mp0) REVERT: A 590 ASP cc_start: 0.7798 (p0) cc_final: 0.7574 (p0) REVERT: A 591 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8294 (mp0) REVERT: B 29 TRP cc_start: 0.7630 (p90) cc_final: 0.7370 (p90) REVERT: B 63 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8337 (tptp) REVERT: B 78 MET cc_start: 0.5454 (ptt) cc_final: 0.5074 (ptt) REVERT: B 232 LEU cc_start: 0.8930 (tp) cc_final: 0.8717 (tp) REVERT: B 245 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8873 (mttt) REVERT: B 336 TYR cc_start: 0.9546 (t80) cc_final: 0.9313 (t80) REVERT: B 389 GLU cc_start: 0.8890 (mt-10) cc_final: 0.7763 (tp30) REVERT: B 435 MET cc_start: 0.9011 (mmt) cc_final: 0.8769 (mmp) REVERT: B 464 ASN cc_start: 0.8992 (t160) cc_final: 0.8515 (t0) REVERT: B 491 MET cc_start: 0.8100 (mmm) cc_final: 0.7711 (tpp) REVERT: B 535 GLU cc_start: 0.8451 (mt-10) cc_final: 0.6777 (mt-10) REVERT: B 580 ASP cc_start: 0.9075 (t0) cc_final: 0.8839 (t0) REVERT: C 29 TRP cc_start: 0.7685 (p90) cc_final: 0.7461 (p90) REVERT: C 63 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8092 (tptp) REVERT: C 245 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8647 (mttt) REVERT: C 330 CYS cc_start: 0.9085 (m) cc_final: 0.8033 (t) REVERT: C 331 MET cc_start: 0.8098 (mtm) cc_final: 0.6610 (mmt) REVERT: C 464 ASN cc_start: 0.8949 (t0) cc_final: 0.8531 (t0) REVERT: C 466 MET cc_start: 0.9302 (mmt) cc_final: 0.9099 (mmm) REVERT: C 491 MET cc_start: 0.8110 (tpt) cc_final: 0.7626 (tpp) REVERT: C 559 TYR cc_start: 0.9395 (t80) cc_final: 0.8741 (t80) REVERT: C 591 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8142 (tm-30) REVERT: D 63 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8028 (tptp) REVERT: D 206 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8597 (tt0) REVERT: D 339 TYR cc_start: 0.9032 (t80) cc_final: 0.8628 (t80) REVERT: D 464 ASN cc_start: 0.8878 (t0) cc_final: 0.8626 (t0) REVERT: D 485 MET cc_start: 0.9021 (mmp) cc_final: 0.8669 (mmp) REVERT: D 559 TYR cc_start: 0.9516 (t80) cc_final: 0.9171 (t80) REVERT: D 570 MET cc_start: 0.8576 (tpt) cc_final: 0.8362 (tpt) REVERT: D 577 MET cc_start: 0.8904 (tpp) cc_final: 0.8554 (tpp) REVERT: D 588 GLU cc_start: 0.6851 (mp0) cc_final: 0.6171 (mp0) REVERT: D 590 ASP cc_start: 0.7787 (p0) cc_final: 0.7398 (p0) REVERT: D 591 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8269 (mp0) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.1320 time to fit residues: 93.2848 Evaluate side-chains 353 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 210 optimal weight: 0.0670 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 0.0970 chunk 226 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074241 restraints weight = 66317.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076248 restraints weight = 38821.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077677 restraints weight = 26543.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078675 restraints weight = 19991.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079008 restraints weight = 16226.055| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19448 Z= 0.131 Angle : 0.726 13.995 26386 Z= 0.352 Chirality : 0.042 0.176 3010 Planarity : 0.004 0.048 3330 Dihedral : 5.374 26.341 2590 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.17), residues: 2353 helix: 0.67 (0.14), residues: 1325 sheet: -4.00 (0.31), residues: 56 loop : -3.07 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 606 TYR 0.011 0.001 TYR B 559 PHE 0.025 0.002 PHE B 434 TRP 0.012 0.001 TRP D 462 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19448) covalent geometry : angle 0.72584 / 0.35 (26386) hydrogen bonds : bond 0.03118 / 2.09 ( 833) hydrogen bonds : angle 4.28654 / 2.94 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 0.753 Fit side-chains TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7321 (p90) cc_final: 0.7046 (p90) REVERT: A 63 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8267 (tptp) REVERT: A 245 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8742 (mttt) REVERT: A 339 TYR cc_start: 0.9086 (t80) cc_final: 0.8746 (t80) REVERT: A 485 MET cc_start: 0.9082 (mmp) cc_final: 0.8121 (mmp) REVERT: A 515 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8438 (tp30) REVERT: A 578 MET cc_start: 0.9115 (mmt) cc_final: 0.8465 (mmm) REVERT: A 588 GLU cc_start: 0.7071 (mp0) cc_final: 0.6277 (mp0) REVERT: A 590 ASP cc_start: 0.7618 (p0) cc_final: 0.7310 (p0) REVERT: A 591 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8160 (mp0) REVERT: B 63 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8334 (tptp) REVERT: B 245 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8727 (mttt) REVERT: B 330 CYS cc_start: 0.9243 (m) cc_final: 0.8893 (m) REVERT: B 389 GLU cc_start: 0.8843 (mt-10) cc_final: 0.7812 (tp30) REVERT: B 464 ASN cc_start: 0.8868 (t160) cc_final: 0.8459 (t0) REVERT: B 491 MET cc_start: 0.7981 (mmm) cc_final: 0.7755 (tpp) REVERT: B 535 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 580 ASP cc_start: 0.8937 (t0) cc_final: 0.8683 (t0) REVERT: C 29 TRP cc_start: 0.7615 (p90) cc_final: 0.7412 (p90) REVERT: C 63 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8085 (tptp) REVERT: C 113 GLU cc_start: 0.7860 (tp30) cc_final: 0.7636 (tp30) REVERT: C 245 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8573 (mttt) REVERT: C 330 CYS cc_start: 0.9072 (m) cc_final: 0.8002 (t) REVERT: C 331 MET cc_start: 0.8027 (mtm) cc_final: 0.6540 (mmt) REVERT: C 442 MET cc_start: 0.8782 (mtp) cc_final: 0.8538 (mtp) REVERT: C 464 ASN cc_start: 0.8876 (t0) cc_final: 0.8452 (t0) REVERT: C 489 ASP cc_start: 0.7949 (t0) cc_final: 0.7721 (t70) REVERT: C 491 MET cc_start: 0.7951 (tpt) cc_final: 0.7571 (tpp) REVERT: C 539 THR cc_start: 0.9532 (m) cc_final: 0.9328 (p) REVERT: C 559 TYR cc_start: 0.9316 (t80) cc_final: 0.9111 (t80) REVERT: C 591 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8086 (tm-30) REVERT: C 592 LEU cc_start: 0.9553 (mm) cc_final: 0.8945 (mm) REVERT: C 596 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8337 (tp40) REVERT: D 63 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7937 (tptp) REVERT: D 78 MET cc_start: 0.4523 (tmm) cc_final: 0.3917 (ptp) REVERT: D 206 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8610 (tt0) REVERT: D 245 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8783 (mttt) REVERT: D 339 TYR cc_start: 0.9065 (t80) cc_final: 0.8819 (t80) REVERT: D 464 ASN cc_start: 0.8910 (t0) cc_final: 0.8594 (t0) REVERT: D 485 MET cc_start: 0.8952 (mmp) cc_final: 0.8627 (mmp) REVERT: D 559 TYR cc_start: 0.9481 (t80) cc_final: 0.9069 (t80) REVERT: D 570 MET cc_start: 0.8570 (tpt) cc_final: 0.8043 (tpt) REVERT: D 588 GLU cc_start: 0.6940 (mp0) cc_final: 0.6198 (mp0) REVERT: D 590 ASP cc_start: 0.7640 (p0) cc_final: 0.7318 (p0) REVERT: D 591 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8246 (mp0) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.1243 time to fit residues: 90.6150 Evaluate side-chains 362 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.087509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073321 restraints weight = 66827.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075252 restraints weight = 39151.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076734 restraints weight = 26846.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077709 restraints weight = 20313.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078375 restraints weight = 16545.051| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19448 Z= 0.159 Angle : 0.756 14.849 26386 Z= 0.369 Chirality : 0.043 0.256 3010 Planarity : 0.004 0.078 3330 Dihedral : 5.417 25.803 2590 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.03 % Favored : 89.93 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2353 helix: 0.62 (0.14), residues: 1340 sheet: -3.85 (0.34), residues: 56 loop : -2.94 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 606 TYR 0.014 0.001 TYR B 559 PHE 0.047 0.002 PHE A 456 TRP 0.017 0.001 TRP D 29 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (19448) covalent geometry : angle 0.75642 / 0.37 (26386) hydrogen bonds : bond 0.03138 / 2.10 ( 833) hydrogen bonds : angle 4.36255 / 2.98 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.712 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7440 (p90) cc_final: 0.7146 (p90) REVERT: A 63 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8262 (tptp) REVERT: A 110 MET cc_start: 0.8210 (mmm) cc_final: 0.7793 (mmm) REVERT: A 245 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8614 (mttt) REVERT: A 339 TYR cc_start: 0.9103 (t80) cc_final: 0.8765 (t80) REVERT: A 515 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8458 (tp30) REVERT: A 530 LEU cc_start: 0.9524 (mp) cc_final: 0.9319 (mp) REVERT: A 590 ASP cc_start: 0.7670 (p0) cc_final: 0.7344 (p0) REVERT: A 591 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8171 (mp0) REVERT: B 63 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8347 (tptp) REVERT: B 232 LEU cc_start: 0.8914 (tp) cc_final: 0.8694 (tp) REVERT: B 245 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8838 (mttt) REVERT: B 330 CYS cc_start: 0.9270 (m) cc_final: 0.8323 (p) REVERT: B 389 GLU cc_start: 0.8879 (mt-10) cc_final: 0.7831 (tp30) REVERT: B 454 MET cc_start: 0.9011 (tpt) cc_final: 0.8808 (tpt) REVERT: B 464 ASN cc_start: 0.8868 (t160) cc_final: 0.8524 (t0) REVERT: B 491 MET cc_start: 0.7995 (mmm) cc_final: 0.7649 (tpp) REVERT: B 535 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 580 ASP cc_start: 0.8959 (t0) cc_final: 0.8705 (t0) REVERT: C 63 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8047 (tptp) REVERT: C 245 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8620 (mttt) REVERT: C 330 CYS cc_start: 0.9067 (m) cc_final: 0.8014 (t) REVERT: C 331 MET cc_start: 0.8125 (mtm) cc_final: 0.6605 (mmt) REVERT: C 464 ASN cc_start: 0.8949 (t0) cc_final: 0.8542 (t0) REVERT: C 466 MET cc_start: 0.9409 (mmm) cc_final: 0.9170 (mmm) REVERT: C 491 MET cc_start: 0.8073 (tpt) cc_final: 0.7743 (tpp) REVERT: C 559 TYR cc_start: 0.9355 (t80) cc_final: 0.9105 (t80) REVERT: C 580 ASP cc_start: 0.8534 (t70) cc_final: 0.8334 (t70) REVERT: C 591 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8107 (tm-30) REVERT: C 596 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8388 (tp40) REVERT: C 597 ILE cc_start: 0.9624 (mm) cc_final: 0.9414 (mm) REVERT: D 63 LYS cc_start: 0.8416 (ttpp) cc_final: 0.7968 (tptp) REVERT: D 206 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8625 (tt0) REVERT: D 245 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8765 (mttt) REVERT: D 339 TYR cc_start: 0.9057 (t80) cc_final: 0.8742 (t80) REVERT: D 454 MET cc_start: 0.8834 (tpt) cc_final: 0.8617 (tpt) REVERT: D 464 ASN cc_start: 0.8885 (t160) cc_final: 0.8630 (t0) REVERT: D 485 MET cc_start: 0.8871 (mmp) cc_final: 0.8261 (mmp) REVERT: D 512 PHE cc_start: 0.9010 (m-10) cc_final: 0.8783 (m-80) REVERT: D 528 MET cc_start: 0.8827 (ttm) cc_final: 0.8288 (ttm) REVERT: D 539 THR cc_start: 0.9654 (m) cc_final: 0.9425 (p) REVERT: D 559 TYR cc_start: 0.9478 (t80) cc_final: 0.8981 (t80) REVERT: D 588 GLU cc_start: 0.6913 (mp0) cc_final: 0.6205 (mp0) REVERT: D 590 ASP cc_start: 0.7661 (p0) cc_final: 0.7272 (p0) REVERT: D 591 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8215 (mp0) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.1214 time to fit residues: 88.9982 Evaluate side-chains 363 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 41 GLN C 197 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.089025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.074535 restraints weight = 65782.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076629 restraints weight = 38163.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078123 restraints weight = 25959.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079158 restraints weight = 19424.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079994 restraints weight = 15798.686| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19448 Z= 0.131 Angle : 0.755 14.681 26386 Z= 0.362 Chirality : 0.043 0.220 3010 Planarity : 0.004 0.066 3330 Dihedral : 5.312 26.336 2590 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2353 helix: 0.63 (0.14), residues: 1340 sheet: -3.74 (0.36), residues: 56 loop : -2.83 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 606 TYR 0.016 0.001 TYR B 339 PHE 0.027 0.002 PHE B 434 TRP 0.014 0.001 TRP D 593 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19448) covalent geometry : angle 0.75504 / 0.36 (26386) hydrogen bonds : bond 0.03022 / 2.03 ( 833) hydrogen bonds : angle 4.31912 / 2.93 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.750 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7394 (p90) cc_final: 0.7090 (p90) REVERT: A 63 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8201 (tptp) REVERT: A 66 LYS cc_start: 0.8176 (mppt) cc_final: 0.7537 (pptt) REVERT: A 110 MET cc_start: 0.8194 (mmm) cc_final: 0.7791 (mmm) REVERT: A 245 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8630 (mttt) REVERT: A 339 TYR cc_start: 0.9123 (t80) cc_final: 0.8779 (t80) REVERT: A 485 MET cc_start: 0.8907 (mmp) cc_final: 0.7913 (mmp) REVERT: A 515 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8451 (tp30) REVERT: A 522 HIS cc_start: 0.8361 (m-70) cc_final: 0.8004 (m-70) REVERT: A 578 MET cc_start: 0.8647 (mmm) cc_final: 0.8060 (mmt) REVERT: A 580 ASP cc_start: 0.8733 (t70) cc_final: 0.8316 (t0) REVERT: A 588 GLU cc_start: 0.7137 (mp0) cc_final: 0.6281 (mp0) REVERT: A 591 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8288 (mp0) REVERT: B 63 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8321 (tptp) REVERT: B 78 MET cc_start: 0.6862 (ttm) cc_final: 0.5631 (ttp) REVERT: B 110 MET cc_start: 0.8570 (mmm) cc_final: 0.7966 (mmm) REVERT: B 245 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8634 (mttt) REVERT: B 330 CYS cc_start: 0.9232 (m) cc_final: 0.8280 (p) REVERT: B 389 GLU cc_start: 0.8887 (mt-10) cc_final: 0.7856 (tp30) REVERT: B 454 MET cc_start: 0.8946 (tpt) cc_final: 0.8730 (tpt) REVERT: B 464 ASN cc_start: 0.8849 (t160) cc_final: 0.8562 (t160) REVERT: B 485 MET cc_start: 0.9289 (mmp) cc_final: 0.8979 (mmp) REVERT: B 535 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 580 ASP cc_start: 0.8935 (t0) cc_final: 0.8658 (t0) REVERT: B 587 HIS cc_start: 0.7650 (t70) cc_final: 0.7309 (m-70) REVERT: B 590 ASP cc_start: 0.7641 (p0) cc_final: 0.7361 (p0) REVERT: B 591 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8212 (mp0) REVERT: C 63 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8081 (tptp) REVERT: C 110 MET cc_start: 0.8327 (mmm) cc_final: 0.7882 (mmm) REVERT: C 245 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8537 (mttt) REVERT: C 330 CYS cc_start: 0.9107 (m) cc_final: 0.8100 (t) REVERT: C 331 MET cc_start: 0.8081 (mtm) cc_final: 0.6577 (mmt) REVERT: C 464 ASN cc_start: 0.8924 (t0) cc_final: 0.8493 (t0) REVERT: C 466 MET cc_start: 0.9466 (mmm) cc_final: 0.9228 (mmm) REVERT: C 491 MET cc_start: 0.7953 (tpt) cc_final: 0.7558 (tpp) REVERT: C 559 TYR cc_start: 0.9361 (t80) cc_final: 0.9106 (t80) REVERT: C 591 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8101 (tm-30) REVERT: C 596 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8354 (tp40) REVERT: D 63 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7958 (tptp) REVERT: D 110 MET cc_start: 0.8312 (mmm) cc_final: 0.7877 (mmm) REVERT: D 206 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8573 (tt0) REVERT: D 245 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8686 (mttt) REVERT: D 339 TYR cc_start: 0.9077 (t80) cc_final: 0.8815 (t80) REVERT: D 466 MET cc_start: 0.9533 (mmp) cc_final: 0.9223 (mmp) REVERT: D 528 MET cc_start: 0.8810 (ttm) cc_final: 0.8264 (ttm) REVERT: D 559 TYR cc_start: 0.9504 (t80) cc_final: 0.8954 (t80) REVERT: D 588 GLU cc_start: 0.6980 (mp0) cc_final: 0.6232 (mp0) REVERT: D 590 ASP cc_start: 0.7597 (p0) cc_final: 0.7262 (p0) REVERT: D 591 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8159 (mp0) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1243 time to fit residues: 91.8382 Evaluate side-chains 371 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 192 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 0.2980 chunk 135 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 582 HIS A 596 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 118 GLN C 206 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 483 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074325 restraints weight = 66252.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076339 restraints weight = 39204.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077762 restraints weight = 26965.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078786 restraints weight = 20400.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079417 restraints weight = 16594.923| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19448 Z= 0.146 Angle : 0.764 14.542 26386 Z= 0.369 Chirality : 0.043 0.207 3010 Planarity : 0.004 0.061 3330 Dihedral : 5.332 25.936 2590 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.10 % Allowed : 0.49 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2353 helix: 0.60 (0.14), residues: 1347 sheet: -3.54 (0.39), residues: 56 loop : -2.91 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 606 TYR 0.013 0.001 TYR B 559 PHE 0.027 0.002 PHE D 434 TRP 0.013 0.001 TRP A 613 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19448) covalent geometry : angle 0.76368 / 0.37 (26386) hydrogen bonds : bond 0.02992 / 2.00 ( 833) hydrogen bonds : angle 4.32908 / 2.95 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7426 (p90) cc_final: 0.7152 (p90) REVERT: A 63 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8258 (tptp) REVERT: A 110 MET cc_start: 0.8253 (mmm) cc_final: 0.7805 (mmm) REVERT: A 339 TYR cc_start: 0.9114 (t80) cc_final: 0.8836 (t80) REVERT: A 515 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8475 (tp30) REVERT: A 522 HIS cc_start: 0.8357 (m-70) cc_final: 0.8036 (m-70) REVERT: A 530 LEU cc_start: 0.9537 (mp) cc_final: 0.9309 (mp) REVERT: A 580 ASP cc_start: 0.8737 (t70) cc_final: 0.8322 (t0) REVERT: A 587 HIS cc_start: 0.7786 (t70) cc_final: 0.7108 (m-70) REVERT: A 588 GLU cc_start: 0.7202 (mp0) cc_final: 0.6304 (mp0) REVERT: A 591 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8224 (mp0) REVERT: B 63 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8359 (tptp) REVERT: B 78 MET cc_start: 0.6875 (ttm) cc_final: 0.5823 (ttp) REVERT: B 110 MET cc_start: 0.8521 (mmm) cc_final: 0.7960 (mmm) REVERT: B 294 GLU cc_start: 0.8420 (pp20) cc_final: 0.8038 (pp20) REVERT: B 330 CYS cc_start: 0.9170 (m) cc_final: 0.8155 (p) REVERT: B 389 GLU cc_start: 0.8954 (mt-10) cc_final: 0.7880 (tp30) REVERT: B 454 MET cc_start: 0.8943 (tpt) cc_final: 0.8499 (tpt) REVERT: B 535 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 63 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8061 (tptp) REVERT: C 110 MET cc_start: 0.8316 (mmm) cc_final: 0.7848 (mmm) REVERT: C 245 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8561 (mttt) REVERT: C 330 CYS cc_start: 0.9121 (m) cc_final: 0.8085 (t) REVERT: C 331 MET cc_start: 0.8167 (mtm) cc_final: 0.6649 (mmt) REVERT: C 464 ASN cc_start: 0.8933 (t0) cc_final: 0.8452 (t0) REVERT: C 466 MET cc_start: 0.9414 (mmm) cc_final: 0.9144 (mmm) REVERT: C 491 MET cc_start: 0.7997 (tpt) cc_final: 0.7634 (tpp) REVERT: C 559 TYR cc_start: 0.9288 (t80) cc_final: 0.9051 (t80) REVERT: C 591 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8116 (tm-30) REVERT: C 596 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8390 (tp40) REVERT: D 63 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7978 (tptp) REVERT: D 110 MET cc_start: 0.8308 (mmm) cc_final: 0.7888 (mmm) REVERT: D 206 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8600 (tt0) REVERT: D 232 LEU cc_start: 0.8787 (tp) cc_final: 0.8579 (tp) REVERT: D 245 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8651 (mttt) REVERT: D 339 TYR cc_start: 0.9046 (t80) cc_final: 0.8753 (t80) REVERT: D 512 PHE cc_start: 0.9107 (m-10) cc_final: 0.8862 (m-80) REVERT: D 528 MET cc_start: 0.8772 (ttm) cc_final: 0.8264 (ttm) REVERT: D 559 TYR cc_start: 0.9489 (t80) cc_final: 0.8902 (t80) REVERT: D 578 MET cc_start: 0.8746 (mmm) cc_final: 0.7358 (mmm) REVERT: D 588 GLU cc_start: 0.6894 (mp0) cc_final: 0.6195 (mp0) REVERT: D 590 ASP cc_start: 0.7613 (p0) cc_final: 0.7273 (p0) REVERT: D 591 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8160 (mp0) outliers start: 2 outliers final: 0 residues processed: 456 average time/residue: 0.1231 time to fit residues: 89.7466 Evaluate side-chains 361 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 151 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 197 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 582 HIS ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074607 restraints weight = 66517.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076703 restraints weight = 38889.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078181 restraints weight = 26521.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079200 restraints weight = 20020.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.079975 restraints weight = 16213.202| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19448 Z= 0.137 Angle : 0.762 14.376 26386 Z= 0.367 Chirality : 0.043 0.195 3010 Planarity : 0.004 0.079 3330 Dihedral : 5.308 26.173 2590 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.17), residues: 2353 helix: 0.65 (0.14), residues: 1339 sheet: -3.41 (0.42), residues: 56 loop : -2.83 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 606 TYR 0.016 0.001 TYR C 339 PHE 0.033 0.002 PHE A 434 TRP 0.015 0.001 TRP D 613 HIS 0.008 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (19448) covalent geometry : angle 0.76216 / 0.37 (26386) hydrogen bonds : bond 0.03001 / 2.00 ( 833) hydrogen bonds : angle 4.31202 / 2.92 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.92 seconds wall clock time: 55 minutes 52.99 seconds (3352.99 seconds total)