Starting phenix.real_space_refine on Sat Jul 4 08:56:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0m_24109/07_2026/7n0m_24109.cif" } resolution = 3.5 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= 0.030 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 B 4 2.79 5 C 12988 2.51 5 N 3304 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19780 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 7.87, per 1000 atoms: 0.40 Number of scatterers: 19780 At special positions: 0 Unit cell: (142.31, 142.31, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 3376 8.00 N 3304 7.00 C 12988 6.00 B 4 5.00 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: 1.70 Conformation dependent library (CDL) restraints added in 828.5 milliseconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 60.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.954A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.908A pdb=" N GLU A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.534A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 166 through 174 removed outlier: 4.183A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.063A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.516A pdb=" N VAL A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.774A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.621A pdb=" N ALA A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.757A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 375 removed outlier: 3.670A pdb=" N MET A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.774A pdb=" N PHE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.586A pdb=" N VAL A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.778A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.707A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 532 through 559 removed outlier: 4.219A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 619 through 650 removed outlier: 4.355A pdb=" N ILE A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 4.530A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.954A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.908A pdb=" N GLU B 91 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.534A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 166 through 174 removed outlier: 4.183A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 4.063A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.516A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.774A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.621A pdb=" N ALA B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.756A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 375 removed outlier: 3.670A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 removed outlier: 3.774A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.585A pdb=" N VAL B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.779A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.707A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 532 through 559 removed outlier: 4.219A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 619 through 650 removed outlier: 4.355A pdb=" N ILE B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 672 removed outlier: 4.531A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.953A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.908A pdb=" N GLU C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.534A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.182A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.063A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.516A pdb=" N VAL C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 262 through 282 removed outlier: 3.775A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.621A pdb=" N ALA C 302 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.757A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.669A pdb=" N MET C 372 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 removed outlier: 3.774A pdb=" N PHE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.586A pdb=" N VAL C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.778A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.707A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 526 through 532 Processing helix chain 'C' and resid 532 through 559 removed outlier: 4.219A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 600 Processing helix chain 'C' and resid 619 through 650 removed outlier: 4.355A pdb=" N ILE C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 672 removed outlier: 4.530A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.954A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.908A pdb=" N GLU D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.534A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 166 through 174 removed outlier: 4.183A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 4.063A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.516A pdb=" N VAL D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 262 through 282 removed outlier: 3.775A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.621A pdb=" N ALA D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.757A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 375 removed outlier: 3.670A pdb=" N MET D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 removed outlier: 3.774A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.586A pdb=" N VAL D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.778A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.707A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 526 through 532 Processing helix chain 'D' and resid 532 through 559 removed outlier: 4.220A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 619 through 650 removed outlier: 4.354A pdb=" N ILE D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 646 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 672 removed outlier: 4.531A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.530A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2844 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: 3.31 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5706 1.33 - 1.45: 3684 1.45 - 1.57: 10726 1.57 - 1.69: 8 1.69 - 1.81: 164 Bond restraints: 20288 Sorted by residual: bond pdb=" CG LEU B 342 " pdb=" CD1 LEU B 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CG LEU D 342 " pdb=" CD1 LEU D 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.48e+00 bond pdb=" CG LEU A 342 " pdb=" CD1 LEU A 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CG LEU C 342 " pdb=" CD1 LEU C 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CB MET A 404 " pdb=" CG MET A 404 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 ... (remaining 20283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 26968 3.01 - 6.03: 509 6.03 - 9.04: 87 9.04 - 12.05: 8 12.05 - 15.06: 4 Bond angle restraints: 27576 Sorted by residual: angle pdb=" N VAL C 348 " pdb=" CA VAL C 348 " pdb=" C VAL C 348 " ideal model delta sigma weight residual 113.53 107.66 5.87 9.80e-01 1.04e+00 3.59e+01 angle pdb=" N VAL B 348 " pdb=" CA VAL B 348 " pdb=" C VAL B 348 " ideal model delta sigma weight residual 113.53 107.66 5.87 9.80e-01 1.04e+00 3.58e+01 angle pdb=" N VAL A 348 " pdb=" CA VAL A 348 " pdb=" C VAL A 348 " ideal model delta sigma weight residual 113.53 107.67 5.86 9.80e-01 1.04e+00 3.57e+01 angle pdb=" N VAL D 348 " pdb=" CA VAL D 348 " pdb=" C VAL D 348 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.55e+01 angle pdb=" CB MET B 404 " pdb=" CG MET B 404 " pdb=" SD MET B 404 " ideal model delta sigma weight residual 112.70 97.64 15.06 3.00e+00 1.11e-01 2.52e+01 ... (remaining 27571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 10333 16.57 - 33.15: 1143 33.15 - 49.72: 272 49.72 - 66.30: 40 66.30 - 82.87: 32 Dihedral angle restraints: 11820 sinusoidal: 4592 harmonic: 7228 Sorted by residual: dihedral pdb=" CA PRO B 699 " pdb=" C PRO B 699 " pdb=" N ASP B 700 " pdb=" CA ASP B 700 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO D 699 " pdb=" C PRO D 699 " pdb=" N ASP D 700 " pdb=" CA ASP D 700 " ideal model delta harmonic sigma weight residual 180.00 155.91 24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO C 699 " pdb=" C PRO C 699 " pdb=" N ASP C 700 " pdb=" CA ASP C 700 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 11817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2046 0.046 - 0.091: 793 0.091 - 0.137: 244 0.137 - 0.182: 49 0.182 - 0.228: 12 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB VAL B 84 " pdb=" CA VAL B 84 " pdb=" CG1 VAL B 84 " pdb=" CG2 VAL B 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL D 84 " pdb=" CA VAL D 84 " pdb=" CG1 VAL D 84 " pdb=" CG2 VAL D 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL A 84 " pdb=" CA VAL A 84 " pdb=" CG1 VAL A 84 " pdb=" CG2 VAL A 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3141 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 162 " -0.019 2.00e-02 2.50e+03 2.00e-02 8.00e+00 pdb=" CG TYR B 162 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 162 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 162 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 162 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 162 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 162 " 0.019 2.00e-02 2.50e+03 2.00e-02 7.97e+00 pdb=" CG TYR D 162 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 162 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 162 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 162 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 162 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 162 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 162 " -0.019 2.00e-02 2.50e+03 2.00e-02 7.96e+00 pdb=" CG TYR C 162 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR C 162 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 162 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 162 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 162 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 162 " 0.003 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5754 2.81 - 3.33: 18489 3.33 - 3.86: 32478 3.86 - 4.38: 35946 4.38 - 4.90: 62301 Nonbonded interactions: 154968 Sorted by model distance: nonbonded pdb=" O PHE D 209 " pdb=" OG SER D 215 " model vdw 2.290 3.040 nonbonded pdb=" O PHE A 209 " pdb=" OG SER A 215 " model vdw 2.291 3.040 nonbonded pdb=" O PHE C 209 " pdb=" OG SER C 215 " model vdw 2.291 3.040 nonbonded pdb=" O PHE B 209 " pdb=" OG SER B 215 " model vdw 2.291 3.040 nonbonded pdb=" NE2 GLN C 452 " pdb=" OE2 GLU C 473 " model vdw 2.337 3.120 ... (remaining 154963 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 20288 Z= 0.363 Angle : 1.056 15.064 27576 Z= 0.537 Chirality : 0.054 0.228 3144 Planarity : 0.006 0.070 3396 Dihedral : 15.183 82.869 7156 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 0.76 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.71 (0.15), residues: 2452 helix: -1.05 (0.13), residues: 1388 sheet: 0.32 (0.66), residues: 64 loop : -3.04 (0.15), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 388 TYR 0.049 0.003 TYR B 162 PHE 0.038 0.003 PHE C 472 TRP 0.030 0.002 TRP B 660 HIS 0.023 0.003 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.36 (20288) covalent geometry : angle 1.05578 / 0.54 (27576) hydrogen bonds : bond 0.15754 / 10.24 ( 972) hydrogen bonds : angle 6.40819 / 4.63 ( 2844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.665 Fit side-chains REVERT: A 145 ASP cc_start: 0.6662 (m-30) cc_final: 0.6210 (m-30) REVERT: A 457 TRP cc_start: 0.8212 (t60) cc_final: 0.7797 (t60) REVERT: B 141 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7423 (tp-100) REVERT: B 145 ASP cc_start: 0.7040 (m-30) cc_final: 0.6572 (m-30) REVERT: B 457 TRP cc_start: 0.7991 (t60) cc_final: 0.7641 (t60) REVERT: B 511 ASN cc_start: 0.8672 (m-40) cc_final: 0.8442 (m-40) REVERT: C 141 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7685 (tp-100) REVERT: C 145 ASP cc_start: 0.6968 (m-30) cc_final: 0.6541 (m-30) REVERT: C 457 TRP cc_start: 0.8018 (t60) cc_final: 0.7670 (t60) REVERT: D 141 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7730 (tp-100) REVERT: D 145 ASP cc_start: 0.6944 (m-30) cc_final: 0.6516 (m-30) REVERT: D 457 TRP cc_start: 0.8012 (t60) cc_final: 0.7645 (t60) outliers start: 12 outliers final: 4 residues processed: 205 average time/residue: 0.1149 time to fit residues: 38.5703 Evaluate side-chains 146 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN A 521 HIS C 521 HIS D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118002 restraints weight = 33957.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120543 restraints weight = 22400.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122223 restraints weight = 17131.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123331 restraints weight = 14362.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123967 restraints weight = 12766.483| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20288 Z= 0.124 Angle : 0.598 10.880 27576 Z= 0.285 Chirality : 0.038 0.117 3144 Planarity : 0.004 0.056 3396 Dihedral : 6.422 64.374 2708 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.96 % Allowed : 8.80 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.18 (0.16), residues: 2452 helix: 0.34 (0.14), residues: 1420 sheet: 0.08 (0.62), residues: 72 loop : -2.64 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 535 TYR 0.019 0.001 TYR B 162 PHE 0.016 0.001 PHE D 476 TRP 0.010 0.001 TRP C 660 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20288) covalent geometry : angle 0.59794 / 0.28 (27576) hydrogen bonds : bond 0.03680 / 2.41 ( 972) hydrogen bonds : angle 4.14586 / 3.02 ( 2844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.485 Fit side-chains REVERT: A 141 GLN cc_start: 0.7645 (tp40) cc_final: 0.7147 (tp-100) REVERT: A 457 TRP cc_start: 0.8077 (t60) cc_final: 0.7718 (t60) REVERT: B 141 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7539 (tp-100) REVERT: B 145 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: B 457 TRP cc_start: 0.7948 (t60) cc_final: 0.7637 (t60) REVERT: C 145 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6407 (m-30) REVERT: C 457 TRP cc_start: 0.7958 (t60) cc_final: 0.7638 (t60) REVERT: D 145 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6484 (m-30) REVERT: D 457 TRP cc_start: 0.7909 (t60) cc_final: 0.7576 (t60) outliers start: 20 outliers final: 14 residues processed: 210 average time/residue: 0.1176 time to fit residues: 40.0757 Evaluate side-chains 173 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 239 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 54 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119466 restraints weight = 33638.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122000 restraints weight = 21757.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123565 restraints weight = 16471.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124711 restraints weight = 13838.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125397 restraints weight = 12208.948| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20288 Z= 0.101 Angle : 0.541 7.089 27576 Z= 0.261 Chirality : 0.037 0.115 3144 Planarity : 0.004 0.055 3396 Dihedral : 5.813 53.522 2708 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.10 % Allowed : 10.99 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.47 (0.17), residues: 2452 helix: 0.96 (0.14), residues: 1416 sheet: 0.44 (0.62), residues: 72 loop : -2.42 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.014 0.001 TYR C 162 PHE 0.009 0.001 PHE D 705 TRP 0.008 0.001 TRP D 660 HIS 0.016 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20288) covalent geometry : angle 0.54144 / 0.26 (27576) hydrogen bonds : bond 0.03223 / 2.13 ( 972) hydrogen bonds : angle 3.82755 / 2.78 ( 2844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.741 Fit side-chains REVERT: A 457 TRP cc_start: 0.8066 (t60) cc_final: 0.7730 (t60) REVERT: A 521 HIS cc_start: 0.5629 (OUTLIER) cc_final: 0.4243 (p90) REVERT: B 141 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7563 (tp-100) REVERT: B 145 ASP cc_start: 0.6984 (m-30) cc_final: 0.6231 (m-30) REVERT: B 457 TRP cc_start: 0.7918 (t60) cc_final: 0.7638 (t60) REVERT: B 521 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4427 (p-80) REVERT: C 141 GLN cc_start: 0.7605 (tp-100) cc_final: 0.6905 (tp-100) REVERT: C 457 TRP cc_start: 0.7939 (t60) cc_final: 0.7636 (t60) REVERT: C 511 ASN cc_start: 0.8610 (m-40) cc_final: 0.8242 (m-40) REVERT: C 521 HIS cc_start: 0.5539 (OUTLIER) cc_final: 0.4271 (p90) REVERT: D 141 GLN cc_start: 0.7597 (tp-100) cc_final: 0.6863 (tp-100) REVERT: D 457 TRP cc_start: 0.7899 (t60) cc_final: 0.7593 (t60) outliers start: 44 outliers final: 23 residues processed: 206 average time/residue: 0.1131 time to fit residues: 39.0355 Evaluate side-chains 181 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 226 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 217 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114536 restraints weight = 34124.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117111 restraints weight = 22844.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118760 restraints weight = 17477.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119815 restraints weight = 14684.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120590 restraints weight = 13102.277| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20288 Z= 0.185 Angle : 0.595 7.213 27576 Z= 0.291 Chirality : 0.039 0.129 3144 Planarity : 0.004 0.061 3396 Dihedral : 5.504 49.734 2708 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.87 % Allowed : 12.57 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.37 (0.17), residues: 2452 helix: 1.04 (0.14), residues: 1416 sheet: 0.16 (0.61), residues: 72 loop : -2.33 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 328 TYR 0.016 0.002 TYR B 228 PHE 0.014 0.001 PHE A 397 TRP 0.010 0.001 TRP A 386 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (20288) covalent geometry : angle 0.59527 / 0.29 (27576) hydrogen bonds : bond 0.03836 / 2.51 ( 972) hydrogen bonds : angle 3.84429 / 2.80 ( 2844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.573 Fit side-chains REVERT: A 141 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7087 (tp-100) REVERT: A 145 ASP cc_start: 0.6294 (m-30) cc_final: 0.5567 (m-30) REVERT: A 457 TRP cc_start: 0.8163 (t60) cc_final: 0.7675 (t60) REVERT: A 512 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 521 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.3973 (p90) REVERT: B 141 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7618 (tp-100) REVERT: B 145 ASP cc_start: 0.7222 (m-30) cc_final: 0.6488 (m-30) REVERT: B 457 TRP cc_start: 0.8103 (t60) cc_final: 0.7618 (t60) REVERT: C 145 ASP cc_start: 0.6930 (m-30) cc_final: 0.6202 (m-30) REVERT: C 457 TRP cc_start: 0.8044 (t60) cc_final: 0.7540 (t60) REVERT: C 512 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 521 HIS cc_start: 0.5596 (OUTLIER) cc_final: 0.4343 (p-80) REVERT: D 457 TRP cc_start: 0.8001 (t60) cc_final: 0.7481 (t60) outliers start: 60 outliers final: 26 residues processed: 210 average time/residue: 0.1074 time to fit residues: 38.1459 Evaluate side-chains 183 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 162 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 198 optimal weight: 0.0970 chunk 239 optimal weight: 0.8980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117342 restraints weight = 33731.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119875 restraints weight = 22266.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121604 restraints weight = 16985.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122645 restraints weight = 14185.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123426 restraints weight = 12664.624| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20288 Z= 0.113 Angle : 0.534 6.488 27576 Z= 0.257 Chirality : 0.037 0.119 3144 Planarity : 0.004 0.057 3396 Dihedral : 5.152 51.437 2708 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.63 % Allowed : 13.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.12 (0.17), residues: 2452 helix: 1.27 (0.14), residues: 1416 sheet: 0.20 (0.63), residues: 72 loop : -2.27 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.015 0.001 TYR A 471 PHE 0.012 0.001 PHE A 472 TRP 0.014 0.001 TRP B 660 HIS 0.010 0.001 HIS C 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (20288) covalent geometry : angle 0.53447 / 0.26 (27576) hydrogen bonds : bond 0.03232 / 2.13 ( 972) hydrogen bonds : angle 3.67555 / 2.67 ( 2844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.507 Fit side-chains REVERT: A 141 GLN cc_start: 0.7789 (tp-100) cc_final: 0.7401 (tp-100) REVERT: A 145 ASP cc_start: 0.6924 (m-30) cc_final: 0.6085 (m-30) REVERT: A 457 TRP cc_start: 0.8036 (t60) cc_final: 0.7583 (t60) REVERT: B 141 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7537 (tp-100) REVERT: B 145 ASP cc_start: 0.7154 (m-30) cc_final: 0.6390 (m-30) REVERT: B 457 TRP cc_start: 0.8021 (t60) cc_final: 0.7577 (t60) REVERT: B 521 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.4835 (p-80) REVERT: B 631 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mm) REVERT: C 457 TRP cc_start: 0.8033 (t60) cc_final: 0.7570 (t60) REVERT: C 512 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8490 (tp) REVERT: C 521 HIS cc_start: 0.5324 (OUTLIER) cc_final: 0.4001 (p90) REVERT: D 457 TRP cc_start: 0.7964 (t60) cc_final: 0.7497 (t60) REVERT: D 521 HIS cc_start: 0.5727 (OUTLIER) cc_final: 0.4913 (p-80) outliers start: 55 outliers final: 34 residues processed: 203 average time/residue: 0.1038 time to fit residues: 36.6784 Evaluate side-chains 195 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 16 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 123 optimal weight: 0.0040 chunk 144 optimal weight: 0.2980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119790 restraints weight = 33961.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122348 restraints weight = 22601.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124017 restraints weight = 17373.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125122 restraints weight = 14631.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125815 restraints weight = 13023.231| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20288 Z= 0.099 Angle : 0.517 7.813 27576 Z= 0.248 Chirality : 0.036 0.119 3144 Planarity : 0.003 0.054 3396 Dihedral : 4.835 52.519 2708 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.01 % Allowed : 14.63 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.14 (0.17), residues: 2452 helix: 1.50 (0.14), residues: 1428 sheet: 0.30 (0.64), residues: 72 loop : -2.24 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 706 TYR 0.016 0.001 TYR A 471 PHE 0.011 0.001 PHE A 472 TRP 0.013 0.001 TRP C 660 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (20288) covalent geometry : angle 0.51732 / 0.25 (27576) hydrogen bonds : bond 0.03021 / 1.99 ( 972) hydrogen bonds : angle 3.57543 / 2.60 ( 2844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 0.800 Fit side-chains REVERT: A 141 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7263 (tp-100) REVERT: A 145 ASP cc_start: 0.7000 (m-30) cc_final: 0.6074 (m-30) REVERT: A 457 TRP cc_start: 0.7953 (t60) cc_final: 0.7499 (t60) REVERT: A 521 HIS cc_start: 0.5720 (OUTLIER) cc_final: 0.4890 (p-80) REVERT: B 141 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7642 (tp-100) REVERT: B 145 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: B 457 TRP cc_start: 0.7942 (t60) cc_final: 0.7489 (t60) REVERT: B 521 HIS cc_start: 0.5712 (OUTLIER) cc_final: 0.4831 (p-80) REVERT: C 457 TRP cc_start: 0.7962 (t60) cc_final: 0.7488 (t60) REVERT: D 457 TRP cc_start: 0.7963 (t60) cc_final: 0.7479 (t60) REVERT: D 521 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.4899 (p-80) outliers start: 63 outliers final: 31 residues processed: 209 average time/residue: 0.1140 time to fit residues: 40.2285 Evaluate side-chains 191 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 16 optimal weight: 0.9990 chunk 128 optimal weight: 0.0060 chunk 132 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 53 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116021 restraints weight = 33431.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118453 restraints weight = 22114.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120089 restraints weight = 16953.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121159 restraints weight = 14199.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121667 restraints weight = 12631.979| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20288 Z= 0.127 Angle : 0.555 8.390 27576 Z= 0.264 Chirality : 0.037 0.187 3144 Planarity : 0.004 0.054 3396 Dihedral : 4.774 51.255 2708 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 15.11 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.18 (0.17), residues: 2452 helix: 1.51 (0.14), residues: 1432 sheet: 0.20 (0.63), residues: 72 loop : -2.17 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.014 0.001 TYR A 471 PHE 0.014 0.001 PHE A 472 TRP 0.014 0.001 TRP C 660 HIS 0.003 0.001 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (20288) covalent geometry : angle 0.55496 / 0.26 (27576) hydrogen bonds : bond 0.03275 / 2.15 ( 972) hydrogen bonds : angle 3.58114 / 2.59 ( 2844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 0.859 Fit side-chains REVERT: A 141 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7296 (tp-100) REVERT: A 145 ASP cc_start: 0.7090 (m-30) cc_final: 0.6158 (m-30) REVERT: A 457 TRP cc_start: 0.7990 (t60) cc_final: 0.7538 (t60) REVERT: A 521 HIS cc_start: 0.5545 (OUTLIER) cc_final: 0.4593 (p-80) REVERT: A 645 MET cc_start: 0.8265 (tpp) cc_final: 0.7906 (tpp) REVERT: B 141 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7660 (tp-100) REVERT: B 145 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: B 457 TRP cc_start: 0.7982 (t60) cc_final: 0.7479 (t60) REVERT: B 521 HIS cc_start: 0.5852 (OUTLIER) cc_final: 0.5038 (p-80) REVERT: C 457 TRP cc_start: 0.7984 (t60) cc_final: 0.7515 (t60) REVERT: C 521 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.4924 (p-80) REVERT: C 645 MET cc_start: 0.8400 (tpp) cc_final: 0.8098 (tpp) REVERT: D 457 TRP cc_start: 0.7985 (t60) cc_final: 0.7497 (t60) outliers start: 64 outliers final: 40 residues processed: 206 average time/residue: 0.1157 time to fit residues: 40.2703 Evaluate side-chains 197 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 130 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 16 optimal weight: 0.0000 chunk 112 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117732 restraints weight = 33409.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120246 restraints weight = 21910.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121921 restraints weight = 16698.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123038 restraints weight = 13949.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123437 restraints weight = 12351.252| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20288 Z= 0.120 Angle : 0.561 9.531 27576 Z= 0.264 Chirality : 0.037 0.201 3144 Planarity : 0.004 0.053 3396 Dihedral : 4.695 51.450 2708 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.49 % Allowed : 15.92 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.24 (0.17), residues: 2452 helix: 1.54 (0.14), residues: 1432 sheet: 0.23 (0.64), residues: 72 loop : -2.13 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.018 0.001 TYR B 471 PHE 0.014 0.001 PHE A 472 TRP 0.013 0.001 TRP C 660 HIS 0.003 0.001 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20288) covalent geometry : angle 0.56124 / 0.26 (27576) hydrogen bonds : bond 0.03219 / 2.12 ( 972) hydrogen bonds : angle 3.56878 / 2.58 ( 2844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.622 Fit side-chains REVERT: A 141 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7283 (tp-100) REVERT: A 145 ASP cc_start: 0.7113 (m-30) cc_final: 0.6145 (m-30) REVERT: A 457 TRP cc_start: 0.8031 (t60) cc_final: 0.7565 (t60) REVERT: A 521 HIS cc_start: 0.5560 (OUTLIER) cc_final: 0.4655 (p-80) REVERT: A 645 MET cc_start: 0.8342 (tpp) cc_final: 0.8035 (tpp) REVERT: B 141 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7586 (tp-100) REVERT: B 145 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6331 (m-30) REVERT: B 457 TRP cc_start: 0.8009 (t60) cc_final: 0.7517 (t60) REVERT: C 457 TRP cc_start: 0.8002 (t60) cc_final: 0.7586 (t60) REVERT: C 521 HIS cc_start: 0.5741 (OUTLIER) cc_final: 0.4862 (p-80) REVERT: D 457 TRP cc_start: 0.8008 (t60) cc_final: 0.7582 (t60) REVERT: D 645 MET cc_start: 0.8200 (tpp) cc_final: 0.7923 (tpp) outliers start: 52 outliers final: 43 residues processed: 196 average time/residue: 0.1128 time to fit residues: 37.4692 Evaluate side-chains 199 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114560 restraints weight = 34052.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117061 restraints weight = 23200.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118671 restraints weight = 18066.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119797 restraints weight = 15314.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120408 restraints weight = 13706.756| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20288 Z= 0.186 Angle : 0.629 9.955 27576 Z= 0.301 Chirality : 0.040 0.185 3144 Planarity : 0.004 0.055 3396 Dihedral : 4.838 49.112 2708 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.72 % Allowed : 16.40 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.07 (0.17), residues: 2452 helix: 1.36 (0.14), residues: 1432 sheet: 0.21 (0.64), residues: 72 loop : -2.14 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 459 TYR 0.019 0.002 TYR B 471 PHE 0.018 0.001 PHE A 472 TRP 0.017 0.001 TRP B 660 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (20288) covalent geometry : angle 0.62879 / 0.30 (27576) hydrogen bonds : bond 0.03774 / 2.48 ( 972) hydrogen bonds : angle 3.72610 / 2.70 ( 2844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.772 Fit side-chains REVERT: A 141 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7455 (tp-100) REVERT: A 145 ASP cc_start: 0.7150 (m-30) cc_final: 0.6136 (m-30) REVERT: A 457 TRP cc_start: 0.8096 (t60) cc_final: 0.7630 (t60) REVERT: A 521 HIS cc_start: 0.5722 (OUTLIER) cc_final: 0.4838 (p-80) REVERT: A 645 MET cc_start: 0.8332 (tpp) cc_final: 0.8056 (tpp) REVERT: B 141 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7649 (tp-100) REVERT: B 145 ASP cc_start: 0.7334 (m-30) cc_final: 0.6536 (m-30) REVERT: B 457 TRP cc_start: 0.8122 (t60) cc_final: 0.7603 (t60) REVERT: C 457 TRP cc_start: 0.8089 (t60) cc_final: 0.7557 (t60) REVERT: C 521 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.4673 (p-80) REVERT: D 457 TRP cc_start: 0.8111 (t60) cc_final: 0.7590 (t60) REVERT: D 645 MET cc_start: 0.8258 (tpp) cc_final: 0.7920 (tpp) outliers start: 57 outliers final: 42 residues processed: 197 average time/residue: 0.1203 time to fit residues: 39.5823 Evaluate side-chains 195 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 212 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 ASN D 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114771 restraints weight = 33905.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117249 restraints weight = 22477.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118901 restraints weight = 17296.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119956 restraints weight = 14521.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120735 restraints weight = 12939.186| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20288 Z= 0.131 Angle : 0.592 10.012 27576 Z= 0.279 Chirality : 0.038 0.187 3144 Planarity : 0.004 0.054 3396 Dihedral : 4.738 50.446 2708 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.29 % Allowed : 16.68 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.19 (0.17), residues: 2452 helix: 1.47 (0.14), residues: 1432 sheet: 0.35 (0.64), residues: 72 loop : -2.10 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 459 TYR 0.020 0.001 TYR B 471 PHE 0.015 0.001 PHE A 472 TRP 0.013 0.001 TRP B 660 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (20288) covalent geometry : angle 0.59175 / 0.28 (27576) hydrogen bonds : bond 0.03380 / 2.23 ( 972) hydrogen bonds : angle 3.64650 / 2.64 ( 2844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.717 Fit side-chains REVERT: A 141 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7421 (tp-100) REVERT: A 145 ASP cc_start: 0.7043 (m-30) cc_final: 0.6024 (m-30) REVERT: A 457 TRP cc_start: 0.8072 (t60) cc_final: 0.7618 (t60) REVERT: A 521 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4748 (p-80) REVERT: A 645 MET cc_start: 0.8344 (tpp) cc_final: 0.8101 (tpp) REVERT: B 141 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7624 (tp-100) REVERT: B 145 ASP cc_start: 0.7212 (m-30) cc_final: 0.6455 (m-30) REVERT: B 457 TRP cc_start: 0.8096 (t60) cc_final: 0.7668 (t60) REVERT: C 457 TRP cc_start: 0.8081 (t60) cc_final: 0.7644 (t60) REVERT: C 521 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4640 (p-80) REVERT: D 457 TRP cc_start: 0.8068 (t60) cc_final: 0.7639 (t60) REVERT: D 521 HIS cc_start: 0.5662 (OUTLIER) cc_final: 0.4873 (p-80) REVERT: D 645 MET cc_start: 0.8311 (tpp) cc_final: 0.7991 (tpp) outliers start: 48 outliers final: 40 residues processed: 186 average time/residue: 0.1142 time to fit residues: 35.5728 Evaluate side-chains 195 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.0070 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 108 optimal weight: 0.0370 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 ASN D 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118985 restraints weight = 33612.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121510 restraints weight = 21905.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123229 restraints weight = 16647.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124375 restraints weight = 13826.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125015 restraints weight = 12203.707| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20288 Z= 0.093 Angle : 0.550 9.654 27576 Z= 0.256 Chirality : 0.036 0.235 3144 Planarity : 0.004 0.052 3396 Dihedral : 4.529 52.687 2708 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 17.40 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.18), residues: 2452 helix: 1.90 (0.14), residues: 1404 sheet: 0.61 (0.64), residues: 72 loop : -1.98 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 459 TYR 0.021 0.001 TYR C 471 PHE 0.009 0.001 PHE B 472 TRP 0.010 0.001 TRP B 660 HIS 0.003 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (20288) covalent geometry : angle 0.54987 / 0.26 (27576) hydrogen bonds : bond 0.02815 / 1.87 ( 972) hydrogen bonds : angle 3.48486 / 2.52 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.32 seconds wall clock time: 46 minutes 42.20 seconds (2802.20 seconds total)