Starting phenix.real_space_refine on Thu Mar 5 05:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0m_24109/03_2026/7n0m_24109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0m_24109/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0m_24109/03_2026/7n0m_24109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0m_24109/03_2026/7n0m_24109.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0m_24109/03_2026/7n0m_24109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0m_24109/03_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-5986/lib/python3.9/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: 7.58, per 1000 atoms: 0.38 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: 1.86 Conformation dependent library (CDL) restraints added in 848.3 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: 0.57 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: 3.18 Time building geometry restraints manager: 2.49 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: 1147 33.15 - 49.72: 272 49.72 - 66.30: 44 66.30 - 82.87: 32 Dihedral angle restraints: 11828 sinusoidal: 4600 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 11825 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.820 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 15.230 82.869 7164 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 covalent geometry : bond 0.00873 (20288) covalent geometry : angle 1.05578 (27576) hydrogen bonds : bond 0.15754 ( 972) hydrogen bonds : angle 6.40819 ( 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 : 0.706 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: 0.1217 time to fit residues: 40.9787 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 : 0.728 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 521 HIS C 521 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117643 restraints weight = 33968.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120173 restraints weight = 22537.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121883 restraints weight = 17217.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122997 restraints weight = 14392.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123638 restraints weight = 12795.337| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1256 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= 0.126 Angle : 0.600 10.447 27576 Z= 0.287 Chirality : 0.038 0.116 3144 Planarity : 0.004 0.056 3396 Dihedral : 6.591 64.977 2716 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.96 % Allowed : 8.46 % Favored : 90.58 % 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: -1.21 (0.16), residues: 2452 helix: 0.32 (0.14), residues: 1420 sheet: 0.06 (0.62), residues: 72 loop : -2.65 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 535 TYR 0.020 0.001 TYR B 162 PHE 0.016 0.001 PHE D 476 TRP 0.010 0.001 TRP A 333 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00296 (20288) covalent geometry : angle 0.59997 (27576) hydrogen bonds : bond 0.03761 ( 972) hydrogen bonds : angle 4.17558 ( 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 215 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.825 Fit side-chains REVERT: A 141 GLN cc_start: 0.7650 (tp40) cc_final: 0.7146 (tp-100) REVERT: A 457 TRP cc_start: 0.8082 (t60) cc_final: 0.7719 (t60) REVERT: B 141 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7538 (tp-100) REVERT: B 145 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: B 457 TRP cc_start: 0.7944 (t60) cc_final: 0.7623 (t60) REVERT: C 145 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: C 457 TRP cc_start: 0.7955 (t60) cc_final: 0.7625 (t60) REVERT: D 145 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6467 (m-30) REVERT: D 457 TRP cc_start: 0.7931 (t60) cc_final: 0.7597 (t60) outliers start: 20 outliers final: 15 residues processed: 207 average time/residue: 0.1279 time to fit residues: 42.7257 Evaluate side-chains 172 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 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: 0.2980 chunk 135 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120328 restraints weight = 34183.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122931 restraints weight = 22211.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124678 restraints weight = 16844.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125728 restraints weight = 14036.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126560 restraints weight = 12476.223| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1689 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= 0.099 Angle : 0.535 6.990 27576 Z= 0.258 Chirality : 0.037 0.113 3144 Planarity : 0.004 0.055 3396 Dihedral : 5.861 57.455 2716 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.72 % Allowed : 11.33 % Favored : 86.95 % 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: -0.49 (0.17), residues: 2452 helix: 0.93 (0.14), residues: 1424 sheet: 0.44 (0.62), residues: 72 loop : -2.41 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 371 TYR 0.014 0.001 TYR D 162 PHE 0.009 0.001 PHE D 705 TRP 0.008 0.001 TRP D 660 HIS 0.018 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00223 (20288) covalent geometry : angle 0.53467 (27576) hydrogen bonds : bond 0.03202 ( 972) hydrogen bonds : angle 3.82615 ( 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 217 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.757 Fit side-chains REVERT: A 457 TRP cc_start: 0.8068 (t60) cc_final: 0.7722 (t60) REVERT: B 141 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7590 (tp-100) REVERT: B 145 ASP cc_start: 0.7031 (m-30) cc_final: 0.6258 (m-30) REVERT: B 457 TRP cc_start: 0.7926 (t60) cc_final: 0.7604 (t60) REVERT: B 511 ASN cc_start: 0.8587 (m-40) cc_final: 0.8249 (m-40) REVERT: B 521 HIS cc_start: 0.5611 (OUTLIER) cc_final: 0.4405 (p-80) REVERT: C 141 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7105 (tp-100) REVERT: C 457 TRP cc_start: 0.7936 (t60) cc_final: 0.7628 (t60) REVERT: C 511 ASN cc_start: 0.8591 (m-40) cc_final: 0.8236 (m-40) REVERT: C 521 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.4189 (p90) REVERT: D 141 GLN cc_start: 0.7667 (tp-100) cc_final: 0.6992 (tp-100) REVERT: D 457 TRP cc_start: 0.7907 (t60) cc_final: 0.7568 (t60) outliers start: 36 outliers final: 19 residues processed: 204 average time/residue: 0.1191 time to fit residues: 40.7935 Evaluate side-chains 174 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 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 651 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 226 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112261 restraints weight = 34185.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114743 restraints weight = 23110.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116374 restraints weight = 17840.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117390 restraints weight = 15058.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118152 restraints weight = 13493.903| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20288 Z= 0.237 Angle : 0.654 7.547 27576 Z= 0.320 Chirality : 0.041 0.139 3144 Planarity : 0.004 0.064 3396 Dihedral : 5.615 47.681 2716 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.25 % Allowed : 12.57 % Favored : 84.18 % 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: -0.50 (0.17), residues: 2452 helix: 0.93 (0.14), residues: 1416 sheet: 0.01 (0.61), residues: 72 loop : -2.37 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.020 0.002 TYR A 228 PHE 0.019 0.002 PHE A 397 TRP 0.012 0.001 TRP D 386 HIS 0.007 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00572 (20288) covalent geometry : angle 0.65380 (27576) hydrogen bonds : bond 0.04222 ( 972) hydrogen bonds : angle 3.96861 ( 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 238 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 0.767 Fit side-chains REVERT: A 141 GLN cc_start: 0.7526 (tp40) cc_final: 0.7175 (tp40) REVERT: A 145 ASP cc_start: 0.6347 (m-30) cc_final: 0.6021 (m-30) REVERT: A 457 TRP cc_start: 0.8194 (t60) cc_final: 0.7648 (t60) REVERT: A 512 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 521 HIS cc_start: 0.5851 (OUTLIER) cc_final: 0.4647 (p90) REVERT: B 141 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7687 (tp-100) REVERT: B 145 ASP cc_start: 0.7261 (m-30) cc_final: 0.6540 (m-30) REVERT: B 457 TRP cc_start: 0.8155 (t60) cc_final: 0.7643 (t60) REVERT: B 512 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 521 HIS cc_start: 0.5648 (OUTLIER) cc_final: 0.4690 (p-80) REVERT: C 121 LEU cc_start: 0.8622 (tt) cc_final: 0.8395 (tt) REVERT: C 141 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7422 (tp-100) REVERT: C 145 ASP cc_start: 0.6997 (m-30) cc_final: 0.6090 (m-30) REVERT: C 457 TRP cc_start: 0.8105 (t60) cc_final: 0.7583 (t60) REVERT: C 512 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 521 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.4125 (p90) REVERT: D 141 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7509 (tp-100) REVERT: D 145 ASP cc_start: 0.6997 (m-30) cc_final: 0.6100 (m-30) REVERT: D 512 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8651 (tp) outliers start: 68 outliers final: 31 residues processed: 221 average time/residue: 0.1168 time to fit residues: 43.0243 Evaluate side-chains 196 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 472 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 483 THR 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 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 HIS 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 483 THR 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 512 LEU Chi-restraints excluded: chain D residue 521 HIS 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: 0.4980 chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3816 r_free = 0.3816 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116070 restraints weight = 33717.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118592 restraints weight = 22417.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120295 restraints weight = 17180.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121407 restraints weight = 14399.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121980 restraints weight = 12786.864| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20288 Z= 0.122 Angle : 0.556 6.865 27576 Z= 0.266 Chirality : 0.037 0.131 3144 Planarity : 0.004 0.059 3396 Dihedral : 5.251 50.186 2716 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.58 % Allowed : 14.34 % Favored : 83.08 % 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: -0.21 (0.17), residues: 2452 helix: 1.19 (0.14), residues: 1416 sheet: 0.17 (0.63), residues: 72 loop : -2.30 (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 0.019 0.001 PHE A 467 TRP 0.013 0.001 TRP D 660 HIS 0.004 0.001 HIS C 521 Details of bonding type rmsd covalent geometry : bond 0.00289 (20288) covalent geometry : angle 0.55645 (27576) hydrogen bonds : bond 0.03386 ( 972) hydrogen bonds : angle 3.74673 ( 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 215 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.745 Fit side-chains REVERT: A 141 GLN cc_start: 0.7692 (tp40) cc_final: 0.7327 (tp-100) REVERT: A 145 ASP cc_start: 0.7058 (m-30) cc_final: 0.6134 (m-30) REVERT: A 457 TRP cc_start: 0.8073 (t60) cc_final: 0.7625 (t60) REVERT: A 521 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.4359 (p90) REVERT: B 141 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7537 (tp-100) REVERT: B 145 ASP cc_start: 0.7225 (m-30) cc_final: 0.6415 (m-30) REVERT: B 457 TRP cc_start: 0.8048 (t60) cc_final: 0.7555 (t60) REVERT: B 631 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8353 (mm) REVERT: C 141 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7205 (tp-100) REVERT: C 145 ASP cc_start: 0.6969 (m-30) cc_final: 0.5957 (m-30) REVERT: C 457 TRP cc_start: 0.7991 (t60) cc_final: 0.7495 (t60) REVERT: C 512 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8511 (tp) REVERT: D 141 GLN cc_start: 0.7735 (tp-100) cc_final: 0.7188 (tp-100) REVERT: D 145 ASP cc_start: 0.6972 (m-30) cc_final: 0.5957 (m-30) REVERT: D 457 TRP cc_start: 0.8080 (t60) cc_final: 0.7577 (t60) REVERT: D 521 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.4997 (p-80) outliers start: 54 outliers final: 32 residues processed: 200 average time/residue: 0.1126 time to fit residues: 38.9058 Evaluate side-chains 197 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 475 LEU 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 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 475 LEU 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 492 MET Chi-restraints excluded: chain C residue 512 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 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: 2.9990 chunk 229 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 209 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3839 r_free = 0.3839 target = 0.140425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117853 restraints weight = 33999.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120357 restraints weight = 22678.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122032 restraints weight = 17501.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123144 restraints weight = 14753.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123598 restraints weight = 13134.799| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20288 Z= 0.115 Angle : 0.541 6.900 27576 Z= 0.261 Chirality : 0.037 0.122 3144 Planarity : 0.004 0.055 3396 Dihedral : 5.034 50.992 2716 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.01 % Allowed : 15.34 % Favored : 81.64 % 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: 0.04 (0.17), residues: 2452 helix: 1.39 (0.14), residues: 1432 sheet: 0.37 (0.64), residues: 72 loop : -2.25 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 706 TYR 0.015 0.001 TYR A 471 PHE 0.012 0.001 PHE A 472 TRP 0.013 0.001 TRP D 660 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00273 (20288) covalent geometry : angle 0.54144 (27576) hydrogen bonds : bond 0.03216 ( 972) hydrogen bonds : angle 3.64881 ( 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 228 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.750 Fit side-chains REVERT: A 141 GLN cc_start: 0.7758 (tp40) cc_final: 0.7355 (tp-100) REVERT: A 145 ASP cc_start: 0.7105 (m-30) cc_final: 0.6182 (m-30) REVERT: A 457 TRP cc_start: 0.8102 (t60) cc_final: 0.7640 (t60) REVERT: A 512 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 521 HIS cc_start: 0.5588 (OUTLIER) cc_final: 0.4443 (p90) REVERT: B 141 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7571 (tp-100) REVERT: B 145 ASP cc_start: 0.7186 (m-30) cc_final: 0.6363 (m-30) REVERT: B 457 TRP cc_start: 0.7989 (t60) cc_final: 0.7492 (t60) REVERT: B 512 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 521 HIS cc_start: 0.5669 (OUTLIER) cc_final: 0.4875 (p-80) REVERT: C 141 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7265 (tp-100) REVERT: C 145 ASP cc_start: 0.7142 (m-30) cc_final: 0.6151 (m-30) REVERT: C 457 TRP cc_start: 0.7992 (t60) cc_final: 0.7528 (t60) REVERT: C 521 HIS cc_start: 0.5464 (OUTLIER) cc_final: 0.4588 (p-80) REVERT: D 141 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7224 (tp-100) REVERT: D 145 ASP cc_start: 0.7101 (m-30) cc_final: 0.6074 (m-30) REVERT: D 457 TRP cc_start: 0.8061 (t60) cc_final: 0.7598 (t60) REVERT: D 521 HIS cc_start: 0.5820 (OUTLIER) cc_final: 0.4957 (p-80) outliers start: 63 outliers final: 34 residues processed: 214 average time/residue: 0.1204 time to fit residues: 43.9203 Evaluate side-chains 200 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 475 LEU Chi-restraints excluded: chain A residue 512 LEU 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 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 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 512 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 16 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 0.0570 chunk 218 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3820 r_free = 0.3820 target = 0.139001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115985 restraints weight = 34238.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118496 restraints weight = 23002.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120132 restraints weight = 17796.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121075 restraints weight = 15080.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121967 restraints weight = 13553.206| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20288 Z= 0.147 Angle : 0.574 8.064 27576 Z= 0.276 Chirality : 0.038 0.172 3144 Planarity : 0.004 0.056 3396 Dihedral : 5.007 49.898 2716 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 16.16 % Favored : 80.83 % 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: 0.02 (0.17), residues: 2452 helix: 1.36 (0.14), residues: 1432 sheet: 0.22 (0.63), residues: 72 loop : -2.22 (0.18), residues: 948 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 0.015 0.001 PHE A 472 TRP 0.015 0.001 TRP D 660 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00353 (20288) covalent geometry : angle 0.57441 (27576) hydrogen bonds : bond 0.03492 ( 972) hydrogen bonds : angle 3.67666 ( 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 227 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.804 Fit side-chains REVERT: A 141 GLN cc_start: 0.7743 (tp40) cc_final: 0.7343 (tp-100) REVERT: A 145 ASP cc_start: 0.7165 (m-30) cc_final: 0.6228 (m-30) REVERT: A 457 TRP cc_start: 0.8070 (t60) cc_final: 0.7652 (t60) REVERT: A 512 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 521 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.4542 (p90) REVERT: B 141 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7544 (tp-100) REVERT: B 145 ASP cc_start: 0.7168 (m-30) cc_final: 0.6406 (m-30) REVERT: B 457 TRP cc_start: 0.8044 (t60) cc_final: 0.7611 (t60) REVERT: B 512 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 521 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.4637 (p-80) REVERT: C 141 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7496 (tp-100) REVERT: C 145 ASP cc_start: 0.7118 (m-30) cc_final: 0.6039 (m-30) REVERT: C 457 TRP cc_start: 0.8051 (t60) cc_final: 0.7620 (t60) REVERT: C 521 HIS cc_start: 0.5575 (OUTLIER) cc_final: 0.4626 (p-80) REVERT: D 141 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7126 (tp-100) REVERT: D 145 ASP cc_start: 0.7123 (m-30) cc_final: 0.5921 (m-30) REVERT: D 457 TRP cc_start: 0.8054 (t60) cc_final: 0.7613 (t60) REVERT: D 521 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5066 (p-80) outliers start: 63 outliers final: 37 residues processed: 214 average time/residue: 0.1241 time to fit residues: 44.6421 Evaluate side-chains 198 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 475 LEU Chi-restraints excluded: chain A residue 512 LEU 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 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 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 512 LEU 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 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 464 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 130 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3831 r_free = 0.3831 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117037 restraints weight = 34097.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119537 restraints weight = 22837.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121209 restraints weight = 17671.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122170 restraints weight = 14930.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122646 restraints weight = 13433.833| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20288 Z= 0.131 Angle : 0.576 8.269 27576 Z= 0.272 Chirality : 0.038 0.202 3144 Planarity : 0.004 0.055 3396 Dihedral : 4.940 50.348 2716 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.63 % Allowed : 16.87 % Favored : 80.50 % 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: 0.11 (0.17), residues: 2452 helix: 1.44 (0.14), residues: 1432 sheet: 0.19 (0.63), residues: 72 loop : -2.18 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.014 0.001 TYR A 471 PHE 0.014 0.001 PHE A 472 TRP 0.013 0.001 TRP D 660 HIS 0.003 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00313 (20288) covalent geometry : angle 0.57605 (27576) hydrogen bonds : bond 0.03336 ( 972) hydrogen bonds : angle 3.65147 ( 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 218 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.720 Fit side-chains REVERT: A 141 GLN cc_start: 0.7761 (tp40) cc_final: 0.7339 (tp-100) REVERT: A 145 ASP cc_start: 0.7246 (m-30) cc_final: 0.6237 (m-30) REVERT: A 457 TRP cc_start: 0.8080 (t60) cc_final: 0.7644 (t60) REVERT: A 512 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 521 HIS cc_start: 0.5675 (OUTLIER) cc_final: 0.4582 (p90) REVERT: B 141 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7470 (tp-100) REVERT: B 145 ASP cc_start: 0.7337 (m-30) cc_final: 0.6495 (m-30) REVERT: B 457 TRP cc_start: 0.8062 (t60) cc_final: 0.7628 (t60) REVERT: B 512 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 521 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.4695 (p-80) REVERT: C 141 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7372 (tp-100) REVERT: C 145 ASP cc_start: 0.7180 (m-30) cc_final: 0.6031 (m-30) REVERT: C 457 TRP cc_start: 0.8068 (t60) cc_final: 0.7619 (t60) REVERT: C 521 HIS cc_start: 0.5567 (OUTLIER) cc_final: 0.4662 (p-80) REVERT: C 645 MET cc_start: 0.8214 (tpp) cc_final: 0.7884 (tpp) REVERT: D 141 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7443 (tp-100) REVERT: D 145 ASP cc_start: 0.7126 (m-30) cc_final: 0.6062 (m-30) REVERT: D 457 TRP cc_start: 0.8041 (t60) cc_final: 0.7649 (t60) REVERT: D 521 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5084 (p-80) REVERT: D 645 MET cc_start: 0.8134 (tpp) cc_final: 0.7860 (tpp) outliers start: 55 outliers final: 40 residues processed: 203 average time/residue: 0.1195 time to fit residues: 41.1431 Evaluate side-chains 205 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS 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 475 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL 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 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 512 LEU 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 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 535 ARG Chi-restraints excluded: chain D residue 543 VAL 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: 1.9990 chunk 214 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3810 r_free = 0.3810 target = 0.137702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115226 restraints weight = 33614.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117694 restraints weight = 22303.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119362 restraints weight = 17224.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120297 restraints weight = 14529.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121131 restraints weight = 13074.801| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20288 Z= 0.148 Angle : 0.597 9.453 27576 Z= 0.283 Chirality : 0.039 0.217 3144 Planarity : 0.004 0.055 3396 Dihedral : 4.954 49.757 2716 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.87 % Allowed : 16.68 % Favored : 80.45 % 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: 0.06 (0.17), residues: 2452 helix: 1.38 (0.14), residues: 1432 sheet: 0.17 (0.63), residues: 72 loop : -2.18 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.013 0.001 TYR A 471 PHE 0.015 0.001 PHE A 472 TRP 0.014 0.001 TRP D 660 HIS 0.004 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00357 (20288) covalent geometry : angle 0.59656 (27576) hydrogen bonds : bond 0.03504 ( 972) hydrogen bonds : angle 3.68202 ( 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 221 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLN cc_start: 0.7692 (tp40) cc_final: 0.7439 (tp-100) REVERT: A 145 ASP cc_start: 0.7096 (m-30) cc_final: 0.6058 (m-30) REVERT: A 457 TRP cc_start: 0.8091 (t60) cc_final: 0.7614 (t60) REVERT: A 512 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 521 HIS cc_start: 0.5715 (OUTLIER) cc_final: 0.4700 (p90) REVERT: A 645 MET cc_start: 0.8279 (tpp) cc_final: 0.7889 (tpp) REVERT: B 141 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7418 (tp-100) REVERT: B 145 ASP cc_start: 0.7263 (m-30) cc_final: 0.6441 (m-30) REVERT: B 457 TRP cc_start: 0.8112 (t60) cc_final: 0.7620 (t60) REVERT: B 512 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 521 HIS cc_start: 0.5602 (OUTLIER) cc_final: 0.4741 (p-80) REVERT: C 141 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7489 (tp-100) REVERT: C 145 ASP cc_start: 0.7120 (m-30) cc_final: 0.6023 (m-30) REVERT: C 457 TRP cc_start: 0.8080 (t60) cc_final: 0.7607 (t60) REVERT: C 521 HIS cc_start: 0.5604 (OUTLIER) cc_final: 0.4753 (p-80) REVERT: C 645 MET cc_start: 0.8335 (tpp) cc_final: 0.8011 (tpp) REVERT: D 141 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7392 (tp-100) REVERT: D 145 ASP cc_start: 0.7096 (m-30) cc_final: 0.5996 (m-30) REVERT: D 457 TRP cc_start: 0.8054 (t60) cc_final: 0.7652 (t60) REVERT: D 521 HIS cc_start: 0.5656 (OUTLIER) cc_final: 0.4813 (p-80) REVERT: D 645 MET cc_start: 0.8279 (tpp) cc_final: 0.7931 (tpp) outliers start: 60 outliers final: 49 residues processed: 209 average time/residue: 0.1165 time to fit residues: 41.2364 Evaluate side-chains 211 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS 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 475 LEU Chi-restraints excluded: chain A residue 512 LEU 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 475 LEU Chi-restraints excluded: chain B residue 512 LEU 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 191 HIS 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 473 GLU 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 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 464 TRP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 473 GLU 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 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: 5.9990 chunk 136 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 101 optimal weight: 0.0870 chunk 173 optimal weight: 4.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.137754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115101 restraints weight = 33784.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117634 restraints weight = 22653.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119261 restraints weight = 17419.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120428 restraints weight = 14677.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121003 restraints weight = 13059.591| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20288 Z= 0.148 Angle : 0.602 8.880 27576 Z= 0.284 Chirality : 0.039 0.218 3144 Planarity : 0.004 0.055 3396 Dihedral : 4.953 49.712 2716 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.96 % Allowed : 16.54 % Favored : 80.50 % 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: 0.05 (0.17), residues: 2452 helix: 1.37 (0.14), residues: 1432 sheet: 0.07 (0.62), residues: 72 loop : -2.18 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 535 TYR 0.013 0.001 TYR A 471 PHE 0.015 0.001 PHE A 472 TRP 0.014 0.001 TRP D 660 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00356 (20288) covalent geometry : angle 0.60223 (27576) hydrogen bonds : bond 0.03522 ( 972) hydrogen bonds : angle 3.68932 ( 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 215 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLN cc_start: 0.7695 (tp40) cc_final: 0.7444 (tp-100) REVERT: A 145 ASP cc_start: 0.7092 (m-30) cc_final: 0.6048 (m-30) REVERT: A 457 TRP cc_start: 0.8083 (t60) cc_final: 0.7683 (t60) REVERT: A 512 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 521 HIS cc_start: 0.5731 (OUTLIER) cc_final: 0.4717 (p90) REVERT: A 645 MET cc_start: 0.8276 (tpp) cc_final: 0.7913 (tpp) REVERT: B 141 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7392 (tp-100) REVERT: B 145 ASP cc_start: 0.7197 (m-30) cc_final: 0.6361 (m-30) REVERT: B 457 TRP cc_start: 0.8101 (t60) cc_final: 0.7598 (t60) REVERT: B 512 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 521 HIS cc_start: 0.5628 (OUTLIER) cc_final: 0.4836 (p-80) REVERT: C 141 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7483 (tp-100) REVERT: C 145 ASP cc_start: 0.7078 (m-30) cc_final: 0.5963 (m-30) REVERT: C 457 TRP cc_start: 0.8089 (t60) cc_final: 0.7662 (t60) REVERT: C 521 HIS cc_start: 0.5610 (OUTLIER) cc_final: 0.4754 (p-80) REVERT: C 607 MET cc_start: 0.7957 (tpt) cc_final: 0.7747 (tpt) REVERT: C 645 MET cc_start: 0.8264 (tpp) cc_final: 0.7989 (tpp) REVERT: D 141 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7505 (tp-100) REVERT: D 145 ASP cc_start: 0.7064 (m-30) cc_final: 0.5929 (m-30) REVERT: D 457 TRP cc_start: 0.8049 (t60) cc_final: 0.7654 (t60) REVERT: D 521 HIS cc_start: 0.5658 (OUTLIER) cc_final: 0.4812 (p-80) REVERT: D 645 MET cc_start: 0.8301 (tpp) cc_final: 0.7979 (tpp) outliers start: 62 outliers final: 52 residues processed: 203 average time/residue: 0.1176 time to fit residues: 40.0674 Evaluate side-chains 207 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS 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 475 LEU Chi-restraints excluded: chain A residue 512 LEU 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 191 HIS 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 473 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 512 LEU 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 191 HIS 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 464 TRP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 473 GLU 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 D residue 162 TYR Chi-restraints excluded: chain D residue 191 HIS 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 464 TRP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 473 GLU 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 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: 0.3980 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116138 restraints weight = 33848.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118614 restraints weight = 22384.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120315 restraints weight = 17173.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121324 restraints weight = 14350.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121947 restraints weight = 12820.056| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20288 Z= 0.110 Angle : 0.571 8.602 27576 Z= 0.266 Chirality : 0.037 0.217 3144 Planarity : 0.004 0.054 3396 Dihedral : 4.846 51.225 2716 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.77 % Allowed : 17.07 % Favored : 80.16 % 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: 0.21 (0.17), residues: 2452 helix: 1.54 (0.14), residues: 1428 sheet: 0.17 (0.63), residues: 72 loop : -2.16 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 535 TYR 0.015 0.001 TYR D 471 PHE 0.011 0.001 PHE B 472 TRP 0.011 0.001 TRP D 660 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00257 (20288) covalent geometry : angle 0.57051 (27576) hydrogen bonds : bond 0.03166 ( 972) hydrogen bonds : angle 3.60489 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.60 seconds wall clock time: 46 minutes 57.72 seconds (2817.72 seconds total)