Starting phenix.real_space_refine on Fri Sep 11 12:39:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1m_8957/09_2026/6e1m_8957.map" } resolution = 3.3 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= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 8 5.49 5 S 40 5.16 5 C 5932 2.51 5 N 1326 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8913 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 179 Unusual residues: {' CA': 5, '3PH': 1, 'PLM': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 176 Unusual residues: {' CA': 2, '3PH': 1, 'PLM': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.12, per 1000 atoms: 0.24 Number of scatterers: 8913 At special positions: 0 Unit cell: (114.266, 91.17, 106.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 40 16.00 P 8 15.00 O 1600 8.00 N 1326 7.00 C 5932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 335.0 milliseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.629A pdb=" N ASP A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.656A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.518A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.988A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.622A pdb=" N TRP A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 removed outlier: 3.536A pdb=" N VAL A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.927A pdb=" N PHE A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.834A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 237 removed outlier: 4.539A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.738A pdb=" N THR A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.652A pdb=" N TYR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.843A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.745A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.583A pdb=" N GLU A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 4.837A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 4.341A pdb=" N SER A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 4.092A pdb=" N PHE A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.642A pdb=" N THR A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.591A pdb=" N PHE A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.521A pdb=" N GLY A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.819A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.792A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.627A pdb=" N GLU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.816A pdb=" N GLY A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 removed outlier: 3.577A pdb=" N SER A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 4.333A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.892A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.504A pdb=" N ALA B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 117 through 136 removed outlier: 4.090A pdb=" N ILE B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.728A pdb=" N TRP B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.536A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.987A pdb=" N PHE B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.870A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 237 removed outlier: 4.624A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.730A pdb=" N THR B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.596A pdb=" N TYR B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.862A pdb=" N VAL B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.092A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 removed outlier: 3.540A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.260A pdb=" N SER B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.642A pdb=" N ASP B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.508A pdb=" N ILE B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.588A pdb=" N PHE B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 629 removed outlier: 3.509A pdb=" N THR B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.812A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 3.775A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 656 " --> pdb=" O PHE B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.526A pdb=" N GLU B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.676A pdb=" N SER B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1251 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: 1.26 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1421 1.31 - 1.43: 2512 1.43 - 1.56: 5069 1.56 - 1.68: 34 1.68 - 1.81: 62 Bond restraints: 9098 Sorted by residual: bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O1P TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 9093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 11915 4.25 - 8.51: 317 8.51 - 12.76: 41 12.76 - 17.02: 4 17.02 - 21.27: 1 Bond angle restraints: 12278 Sorted by residual: angle pdb=" N LEU A 610 " pdb=" CA LEU A 610 " pdb=" C LEU A 610 " ideal model delta sigma weight residual 110.80 95.78 15.02 2.13e+00 2.20e-01 4.97e+01 angle pdb=" C LEU A 609 " pdb=" N LEU A 610 " pdb=" CA LEU A 610 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" CA LEU A 610 " pdb=" CB LEU A 610 " pdb=" CG LEU A 610 " ideal model delta sigma weight residual 116.30 137.57 -21.27 3.50e+00 8.16e-02 3.69e+01 angle pdb=" C THR B 263 " pdb=" N THR B 264 " pdb=" CA THR B 264 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C THR A 263 " pdb=" N THR A 264 " pdb=" CA THR A 264 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.89e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 4619 13.95 - 27.89: 504 27.89 - 41.84: 128 41.84 - 55.78: 65 55.78 - 69.73: 38 Dihedral angle restraints: 5354 sinusoidal: 2192 harmonic: 3162 Sorted by residual: dihedral pdb=" CA PHE B 611 " pdb=" C PHE B 611 " pdb=" N ASN B 612 " pdb=" CA ASN B 612 " ideal model delta harmonic sigma weight residual 180.00 -128.46 -51.54 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PHE A 611 " pdb=" C PHE A 611 " pdb=" N ASN A 612 " pdb=" CA ASN A 612 " ideal model delta harmonic sigma weight residual -180.00 -132.19 -47.81 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 139.62 40.38 0 5.00e+00 4.00e-02 6.52e+01 ... (remaining 5351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1049 0.083 - 0.166: 273 0.166 - 0.249: 35 0.249 - 0.333: 8 0.333 - 0.416: 5 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE A 649 " pdb=" CA ILE A 649 " pdb=" CG1 ILE A 649 " pdb=" CG2 ILE A 649 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 1367 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 305 " -0.020 2.00e-02 2.50e+03 2.36e-02 1.12e+01 pdb=" CG TYR A 305 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 305 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 305 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 305 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 305 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 305 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 305 " -0.022 2.00e-02 2.50e+03 2.33e-02 1.09e+01 pdb=" CG TYR B 305 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B 305 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 305 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 305 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 305 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 305 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 305 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 106 " 0.034 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 106 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 106 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 106 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 106 " 0.009 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 81 2.56 - 3.15: 7067 3.15 - 3.73: 13320 3.73 - 4.32: 19471 4.32 - 4.90: 31248 Nonbonded interactions: 71187 Sorted by model distance: nonbonded pdb=" OH TYR B 114 " pdb=" OD2 ASP B 615 " model vdw 1.976 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OD2 ASP A 615 " model vdw 2.001 3.040 nonbonded pdb=" OH TYR A 305 " pdb=" OE2 GLU A 673 " model vdw 2.043 3.040 nonbonded pdb=" OH TYR B 305 " pdb=" OE2 GLU B 673 " model vdw 2.078 3.040 nonbonded pdb=" O TYR A 579 " pdb=" OH TYR A 651 " model vdw 2.151 3.040 ... (remaining 71182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 802 or resid 806 through 809)) selection = (chain 'B' and (resid 22 through 802 or resid 806 through 809)) } 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 individual isotropic 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.840 Find NCS groups from input model: 0.170 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.018 0.139 9107 Z= 0.768 Angle : 1.611 21.272 12278 Z= 0.790 Chirality : 0.079 0.416 1370 Planarity : 0.009 0.073 1500 Dihedral : 14.908 69.726 3310 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.41 % Favored : 91.49 % Rotamer: Outliers : 0.11 % Allowed : 1.23 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.95 (0.17), residues: 1046 helix: -4.07 (0.10), residues: 718 sheet: None (None), residues: 0 loop : -3.05 (0.29), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 700 TYR 0.058 0.007 TYR A 305 PHE 0.042 0.006 PHE B 652 TRP 0.034 0.006 TRP B 632 HIS 0.008 0.005 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.01786 / 0.77 ( 9098) covalent geometry : angle 1.61104 / 0.79 (12278) hydrogen bonds : bond 0.31829 / 20.57 ( 429) hydrogen bonds : angle 11.59121 / 7.85 ( 1251) Misc. bond : bond 0.00485 / 0.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7170 (t70) cc_final: 0.6879 (t70) REVERT: A 43 ASP cc_start: 0.8658 (m-30) cc_final: 0.8315 (m-30) REVERT: A 115 LEU cc_start: 0.8069 (mt) cc_final: 0.7823 (mt) REVERT: A 119 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 204 ASP cc_start: 0.7425 (m-30) cc_final: 0.6986 (m-30) REVERT: A 210 SER cc_start: 0.8445 (m) cc_final: 0.8069 (p) REVERT: A 319 MET cc_start: 0.7973 (tpt) cc_final: 0.7490 (tpt) REVERT: A 324 ARG cc_start: 0.5677 (tpt-90) cc_final: 0.5353 (mtp180) REVERT: A 388 PHE cc_start: 0.8078 (t80) cc_final: 0.7832 (t80) REVERT: A 607 ASP cc_start: 0.8407 (t70) cc_final: 0.7978 (t70) REVERT: A 634 VAL cc_start: 0.8995 (t) cc_final: 0.8663 (m) REVERT: A 637 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6835 (tm-30) REVERT: A 673 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 677 THR cc_start: 0.7191 (m) cc_final: 0.6903 (p) REVERT: A 682 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6409 (tp30) REVERT: B 107 TYR cc_start: 0.5114 (p90) cc_final: 0.4476 (m-10) REVERT: B 204 ASP cc_start: 0.7273 (m-30) cc_final: 0.6972 (m-30) REVERT: B 210 SER cc_start: 0.8468 (m) cc_final: 0.8127 (p) REVERT: B 255 LEU cc_start: 0.8735 (tp) cc_final: 0.8497 (tp) REVERT: B 319 MET cc_start: 0.7939 (tpt) cc_final: 0.7605 (tpt) REVERT: B 324 ARG cc_start: 0.5538 (tpt-90) cc_final: 0.5301 (mtp180) REVERT: B 338 LYS cc_start: 0.8773 (mttt) cc_final: 0.7596 (tptt) REVERT: B 384 ASN cc_start: 0.6237 (t0) cc_final: 0.5844 (t0) REVERT: B 607 ASP cc_start: 0.8500 (t0) cc_final: 0.8284 (t0) REVERT: B 626 LEU cc_start: 0.8728 (mt) cc_final: 0.8523 (mp) REVERT: B 634 VAL cc_start: 0.8841 (t) cc_final: 0.8489 (m) REVERT: B 673 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 677 THR cc_start: 0.7336 (m) cc_final: 0.7055 (p) outliers start: 1 outliers final: 1 residues processed: 290 average time/residue: 0.0865 time to fit residues: 34.6737 Evaluate side-chains 211 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 242 GLN A 585 GLN A 618 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 242 GLN B 585 GLN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.228052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.175505 restraints weight = 9380.903| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.22 r_work: 0.3869 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9107 Z= 0.197 Angle : 0.815 12.787 12278 Z= 0.418 Chirality : 0.044 0.196 1370 Planarity : 0.006 0.065 1500 Dihedral : 15.165 59.961 1434 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.34 % Allowed : 9.26 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.22), residues: 1046 helix: -2.16 (0.16), residues: 720 sheet: None (None), residues: 0 loop : -2.57 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 200 TYR 0.025 0.003 TYR B 305 PHE 0.023 0.002 PHE B 624 TRP 0.019 0.002 TRP B 92 HIS 0.006 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 9098) covalent geometry : angle 0.81463 / 0.42 (12278) hydrogen bonds : bond 0.05557 / 3.45 ( 429) hydrogen bonds : angle 5.57394 / 3.83 ( 1251) Misc. bond : bond 0.00197 / 0.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6911 (t70) cc_final: 0.6655 (t70) REVERT: A 115 LEU cc_start: 0.8291 (mt) cc_final: 0.7894 (mt) REVERT: A 119 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6861 (tm-30) REVERT: A 166 ASP cc_start: 0.8178 (t0) cc_final: 0.7500 (t0) REVERT: A 200 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7972 (ttp-170) REVERT: A 210 SER cc_start: 0.8580 (m) cc_final: 0.8095 (p) REVERT: A 319 MET cc_start: 0.8284 (tpt) cc_final: 0.7808 (tpt) REVERT: A 324 ARG cc_start: 0.5594 (tpt-90) cc_final: 0.5374 (mmm160) REVERT: A 607 ASP cc_start: 0.8154 (t70) cc_final: 0.7674 (m-30) REVERT: A 626 LEU cc_start: 0.9119 (mt) cc_final: 0.8918 (mp) REVERT: A 634 VAL cc_start: 0.8960 (t) cc_final: 0.8660 (m) REVERT: A 656 TYR cc_start: 0.8668 (t80) cc_final: 0.8018 (t80) REVERT: A 660 ILE cc_start: 0.6392 (mm) cc_final: 0.5769 (tt) REVERT: A 677 THR cc_start: 0.7160 (m) cc_final: 0.6689 (p) REVERT: A 678 GLU cc_start: 0.6777 (mp0) cc_final: 0.6211 (mp0) REVERT: A 682 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6337 (tp30) REVERT: B 115 LEU cc_start: 0.8093 (mt) cc_final: 0.7729 (mt) REVERT: B 166 ASP cc_start: 0.8194 (t0) cc_final: 0.7592 (t0) REVERT: B 210 SER cc_start: 0.8617 (m) cc_final: 0.8186 (p) REVERT: B 319 MET cc_start: 0.8272 (tpt) cc_final: 0.7913 (tpt) REVERT: B 324 ARG cc_start: 0.5644 (tpt-90) cc_final: 0.5362 (mmm160) REVERT: B 338 LYS cc_start: 0.8821 (mttt) cc_final: 0.7634 (tptt) REVERT: B 385 LYS cc_start: 0.7355 (ttmt) cc_final: 0.6839 (pttt) REVERT: B 607 ASP cc_start: 0.8298 (t0) cc_final: 0.7973 (t0) REVERT: B 677 THR cc_start: 0.7393 (m) cc_final: 0.7068 (p) outliers start: 21 outliers final: 12 residues processed: 252 average time/residue: 0.0903 time to fit residues: 31.8136 Evaluate side-chains 230 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 134 HIS A 257 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.234250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183153 restraints weight = 9352.026| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.31 r_work: 0.3949 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9107 Z= 0.147 Angle : 0.706 10.829 12278 Z= 0.355 Chirality : 0.042 0.143 1370 Planarity : 0.005 0.066 1500 Dihedral : 13.288 60.219 1434 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.23 % Allowed : 11.05 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.51 (0.24), residues: 1046 helix: -1.26 (0.17), residues: 726 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.021 0.002 TYR B 141 PHE 0.020 0.001 PHE B 554 TRP 0.016 0.001 TRP B 92 HIS 0.007 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9098) covalent geometry : angle 0.70556 / 0.35 (12278) hydrogen bonds : bond 0.04229 / 2.60 ( 429) hydrogen bonds : angle 4.84853 / 3.33 ( 1251) Misc. bond : bond 0.00136 / 0.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8425 (pptt) cc_final: 0.8135 (ptpp) REVERT: A 96 ASN cc_start: 0.7959 (p0) cc_final: 0.7545 (p0) REVERT: A 115 LEU cc_start: 0.8192 (mt) cc_final: 0.7784 (mt) REVERT: A 119 GLU cc_start: 0.7907 (mm-30) cc_final: 0.6955 (tm-30) REVERT: A 166 ASP cc_start: 0.8208 (t0) cc_final: 0.7602 (t0) REVERT: A 200 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7932 (ttp-170) REVERT: A 210 SER cc_start: 0.8554 (m) cc_final: 0.8119 (p) REVERT: A 319 MET cc_start: 0.8273 (tpt) cc_final: 0.7917 (tpt) REVERT: A 324 ARG cc_start: 0.5514 (tpt-90) cc_final: 0.5281 (mtp180) REVERT: A 388 PHE cc_start: 0.7903 (t80) cc_final: 0.7442 (t80) REVERT: A 634 VAL cc_start: 0.8917 (t) cc_final: 0.8643 (m) REVERT: A 676 PHE cc_start: 0.7685 (m-10) cc_final: 0.7255 (m-10) REVERT: A 677 THR cc_start: 0.7048 (m) cc_final: 0.6534 (p) REVERT: A 678 GLU cc_start: 0.6766 (mp0) cc_final: 0.6093 (mp0) REVERT: A 682 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6417 (tp30) REVERT: B 115 LEU cc_start: 0.7998 (mt) cc_final: 0.7684 (mt) REVERT: B 141 TYR cc_start: 0.8710 (p90) cc_final: 0.8449 (p90) REVERT: B 166 ASP cc_start: 0.8250 (t0) cc_final: 0.7720 (t0) REVERT: B 210 SER cc_start: 0.8655 (m) cc_final: 0.8275 (p) REVERT: B 319 MET cc_start: 0.8275 (tpt) cc_final: 0.7869 (tpt) REVERT: B 324 ARG cc_start: 0.5535 (tpt-90) cc_final: 0.5063 (mtp180) REVERT: B 338 LYS cc_start: 0.8788 (mttt) cc_final: 0.7654 (tptt) REVERT: B 386 ASP cc_start: 0.7804 (t0) cc_final: 0.7601 (t0) REVERT: B 387 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7438 (mp0) REVERT: B 607 ASP cc_start: 0.8101 (t0) cc_final: 0.7543 (m-30) REVERT: B 663 LEU cc_start: 0.8618 (mt) cc_final: 0.8309 (mt) REVERT: B 677 THR cc_start: 0.7343 (m) cc_final: 0.7018 (p) REVERT: B 682 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6339 (tp30) outliers start: 20 outliers final: 14 residues processed: 248 average time/residue: 0.0901 time to fit residues: 31.3192 Evaluate side-chains 227 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 346 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.234328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.181785 restraints weight = 9489.345| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.24 r_work: 0.3932 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9107 Z= 0.154 Angle : 0.688 9.020 12278 Z= 0.343 Chirality : 0.042 0.192 1370 Planarity : 0.005 0.066 1500 Dihedral : 12.486 62.925 1434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.79 % Allowed : 13.84 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.80 (0.25), residues: 1046 helix: -0.72 (0.18), residues: 728 sheet: None (None), residues: 0 loop : -2.06 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.021 0.002 TYR A 216 PHE 0.028 0.002 PHE A 65 TRP 0.016 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9098) covalent geometry : angle 0.68845 / 0.34 (12278) hydrogen bonds : bond 0.03846 / 2.35 ( 429) hydrogen bonds : angle 4.59619 / 3.15 ( 1251) Misc. bond : bond 0.00136 / 0.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8494 (pptt) cc_final: 0.8224 (ptpp) REVERT: A 115 LEU cc_start: 0.8241 (mt) cc_final: 0.7856 (mt) REVERT: A 119 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6889 (tm-30) REVERT: A 137 PHE cc_start: 0.8892 (t80) cc_final: 0.8565 (t80) REVERT: A 153 ASN cc_start: 0.8191 (m110) cc_final: 0.7924 (m110) REVERT: A 166 ASP cc_start: 0.8165 (t0) cc_final: 0.7684 (t0) REVERT: A 200 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7944 (ttp-170) REVERT: A 210 SER cc_start: 0.8093 (m) cc_final: 0.7682 (p) REVERT: A 319 MET cc_start: 0.8248 (tpt) cc_final: 0.7837 (tpt) REVERT: A 324 ARG cc_start: 0.5421 (tpt-90) cc_final: 0.5113 (mtp180) REVERT: A 388 PHE cc_start: 0.7994 (t80) cc_final: 0.7618 (t80) REVERT: A 634 VAL cc_start: 0.8939 (t) cc_final: 0.8670 (m) REVERT: A 682 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6364 (tp30) REVERT: B 96 ASN cc_start: 0.7919 (p0) cc_final: 0.7509 (p0) REVERT: B 115 LEU cc_start: 0.8011 (mt) cc_final: 0.7716 (mt) REVERT: B 137 PHE cc_start: 0.8867 (t80) cc_final: 0.8424 (t80) REVERT: B 166 ASP cc_start: 0.8206 (t0) cc_final: 0.7714 (t0) REVERT: B 210 SER cc_start: 0.8443 (m) cc_final: 0.8103 (p) REVERT: B 319 MET cc_start: 0.8179 (tpt) cc_final: 0.7769 (tpt) REVERT: B 324 ARG cc_start: 0.5394 (tpt-90) cc_final: 0.5071 (mtp180) REVERT: B 338 LYS cc_start: 0.8741 (mttt) cc_final: 0.7580 (tptp) REVERT: B 566 MET cc_start: 0.8838 (mmp) cc_final: 0.8620 (mmm) REVERT: B 607 ASP cc_start: 0.7974 (t0) cc_final: 0.7441 (m-30) REVERT: B 663 LEU cc_start: 0.8499 (mt) cc_final: 0.8226 (mt) REVERT: B 677 THR cc_start: 0.7405 (m) cc_final: 0.7027 (p) REVERT: B 682 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6265 (tp30) outliers start: 25 outliers final: 16 residues processed: 231 average time/residue: 0.0927 time to fit residues: 29.8832 Evaluate side-chains 220 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 585 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.234286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181739 restraints weight = 9432.484| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.12 r_work: 0.3945 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9107 Z= 0.153 Angle : 0.683 11.905 12278 Z= 0.338 Chirality : 0.042 0.139 1370 Planarity : 0.004 0.066 1500 Dihedral : 12.048 62.013 1434 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.46 % Allowed : 14.84 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.34 (0.25), residues: 1046 helix: -0.36 (0.18), residues: 730 sheet: None (None), residues: 0 loop : -1.92 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 398 TYR 0.021 0.002 TYR A 216 PHE 0.027 0.001 PHE A 65 TRP 0.017 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9098) covalent geometry : angle 0.68298 / 0.34 (12278) hydrogen bonds : bond 0.03642 / 2.24 ( 429) hydrogen bonds : angle 4.45380 / 3.07 ( 1251) Misc. bond : bond 0.00134 / 0.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8152 (tppt) cc_final: 0.7746 (ttpt) REVERT: A 115 LEU cc_start: 0.8234 (mt) cc_final: 0.7814 (mt) REVERT: A 119 GLU cc_start: 0.7920 (mm-30) cc_final: 0.6902 (tm-30) REVERT: A 137 PHE cc_start: 0.8917 (t80) cc_final: 0.8474 (t80) REVERT: A 153 ASN cc_start: 0.8325 (m110) cc_final: 0.8095 (m110) REVERT: A 166 ASP cc_start: 0.8162 (t0) cc_final: 0.7702 (t0) REVERT: A 200 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7933 (ttp-170) REVERT: A 210 SER cc_start: 0.8147 (m) cc_final: 0.7795 (p) REVERT: A 319 MET cc_start: 0.8182 (tpt) cc_final: 0.7800 (tpt) REVERT: A 324 ARG cc_start: 0.5500 (tpt-90) cc_final: 0.5205 (mtp180) REVERT: A 388 PHE cc_start: 0.8056 (t80) cc_final: 0.7662 (t80) REVERT: A 637 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 660 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5315 (tp) REVERT: A 663 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 682 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6406 (tp30) REVERT: B 94 GLU cc_start: 0.6211 (tt0) cc_final: 0.4000 (tt0) REVERT: B 115 LEU cc_start: 0.8066 (mt) cc_final: 0.7773 (mt) REVERT: B 137 PHE cc_start: 0.8892 (t80) cc_final: 0.8477 (t80) REVERT: B 166 ASP cc_start: 0.8227 (t0) cc_final: 0.7762 (t0) REVERT: B 210 SER cc_start: 0.8228 (m) cc_final: 0.7904 (p) REVERT: B 319 MET cc_start: 0.8085 (tpt) cc_final: 0.7715 (tpt) REVERT: B 324 ARG cc_start: 0.5398 (tpt-90) cc_final: 0.5035 (mtp180) REVERT: B 338 LYS cc_start: 0.8714 (mttt) cc_final: 0.7539 (tptp) REVERT: B 607 ASP cc_start: 0.7867 (t0) cc_final: 0.7566 (m-30) REVERT: B 682 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6249 (tp30) outliers start: 31 outliers final: 21 residues processed: 223 average time/residue: 0.0904 time to fit residues: 28.1750 Evaluate side-chains 220 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN ** A 612 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 = 0.4601 r_free = 0.4601 target = 0.234717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.184581 restraints weight = 9399.588| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.21 r_work: 0.3957 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9107 Z= 0.148 Angle : 0.676 11.726 12278 Z= 0.333 Chirality : 0.041 0.144 1370 Planarity : 0.004 0.065 1500 Dihedral : 11.758 62.836 1434 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.68 % Allowed : 14.96 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.95 (0.26), residues: 1046 helix: -0.08 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.68 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.035 0.002 TYR A 305 PHE 0.017 0.001 PHE B 554 TRP 0.018 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9098) covalent geometry : angle 0.67559 / 0.33 (12278) hydrogen bonds : bond 0.03530 / 2.17 ( 429) hydrogen bonds : angle 4.38102 / 3.01 ( 1251) Misc. bond : bond 0.00129 / 0.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8173 (tppt) cc_final: 0.7811 (ttpt) REVERT: A 115 LEU cc_start: 0.8163 (mt) cc_final: 0.7712 (mt) REVERT: A 119 GLU cc_start: 0.7865 (mm-30) cc_final: 0.6810 (tm-30) REVERT: A 137 PHE cc_start: 0.8915 (t80) cc_final: 0.8468 (t80) REVERT: A 153 ASN cc_start: 0.8378 (m110) cc_final: 0.8171 (m110) REVERT: A 166 ASP cc_start: 0.8190 (t0) cc_final: 0.7722 (t0) REVERT: A 200 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7916 (ttp-170) REVERT: A 210 SER cc_start: 0.8141 (m) cc_final: 0.7732 (p) REVERT: A 319 MET cc_start: 0.8081 (tpt) cc_final: 0.7734 (tpt) REVERT: A 324 ARG cc_start: 0.5444 (tpt-90) cc_final: 0.5143 (mtp180) REVERT: A 388 PHE cc_start: 0.8043 (t80) cc_final: 0.7675 (t80) REVERT: A 660 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5192 (tp) REVERT: A 663 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 682 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6453 (tp30) REVERT: B 95 LYS cc_start: 0.8051 (tppt) cc_final: 0.7618 (ttpt) REVERT: B 137 PHE cc_start: 0.8909 (t80) cc_final: 0.8518 (t80) REVERT: B 166 ASP cc_start: 0.8329 (t0) cc_final: 0.7828 (t0) REVERT: B 210 SER cc_start: 0.8268 (m) cc_final: 0.7934 (p) REVERT: B 306 ASP cc_start: 0.8791 (t0) cc_final: 0.8309 (t0) REVERT: B 319 MET cc_start: 0.8056 (tpt) cc_final: 0.7709 (tpt) REVERT: B 324 ARG cc_start: 0.5410 (tpt-90) cc_final: 0.5082 (mtp180) REVERT: B 335 ASP cc_start: 0.6823 (m-30) cc_final: 0.5954 (t70) REVERT: B 338 LYS cc_start: 0.8670 (mttt) cc_final: 0.7759 (tptp) REVERT: B 607 ASP cc_start: 0.7808 (t0) cc_final: 0.7533 (m-30) REVERT: B 682 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6187 (tp30) outliers start: 33 outliers final: 23 residues processed: 223 average time/residue: 0.0877 time to fit residues: 27.5126 Evaluate side-chains 219 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 68 optimal weight: 0.0030 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.236671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.184101 restraints weight = 9451.128| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.24 r_work: 0.3983 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9107 Z= 0.128 Angle : 0.645 10.738 12278 Z= 0.319 Chirality : 0.041 0.143 1370 Planarity : 0.005 0.071 1500 Dihedral : 11.218 64.652 1434 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.24 % Allowed : 15.62 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.26), residues: 1046 helix: 0.16 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 69 TYR 0.027 0.002 TYR A 305 PHE 0.016 0.001 PHE B 554 TRP 0.019 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9098) covalent geometry : angle 0.64520 / 0.32 (12278) hydrogen bonds : bond 0.03381 / 2.09 ( 429) hydrogen bonds : angle 4.27606 / 2.95 ( 1251) Misc. bond : bond 0.00118 / 0.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8006 (p0) cc_final: 0.7672 (p0) REVERT: A 111 GLU cc_start: 0.7401 (tp30) cc_final: 0.7031 (tt0) REVERT: A 115 LEU cc_start: 0.8083 (mt) cc_final: 0.7644 (mt) REVERT: A 119 GLU cc_start: 0.7912 (mm-30) cc_final: 0.6808 (tm-30) REVERT: A 137 PHE cc_start: 0.8909 (t80) cc_final: 0.8456 (t80) REVERT: A 153 ASN cc_start: 0.8399 (m110) cc_final: 0.8189 (m110) REVERT: A 166 ASP cc_start: 0.8347 (t0) cc_final: 0.7744 (t0) REVERT: A 200 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7956 (ttp-170) REVERT: A 210 SER cc_start: 0.8186 (m) cc_final: 0.7840 (p) REVERT: A 213 LEU cc_start: 0.9131 (mm) cc_final: 0.8841 (mm) REVERT: A 224 MET cc_start: 0.8559 (mtm) cc_final: 0.8264 (mtm) REVERT: A 272 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8700 (mm) REVERT: A 319 MET cc_start: 0.8102 (tpt) cc_final: 0.7759 (tpt) REVERT: A 324 ARG cc_start: 0.5305 (tpt-90) cc_final: 0.5009 (mtp180) REVERT: A 632 TRP cc_start: 0.8659 (p-90) cc_final: 0.7910 (p-90) REVERT: A 660 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.4960 (tp) REVERT: A 663 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 673 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 95 LYS cc_start: 0.8027 (tppt) cc_final: 0.7663 (ttpt) REVERT: B 137 PHE cc_start: 0.8914 (t80) cc_final: 0.8481 (t80) REVERT: B 142 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 166 ASP cc_start: 0.8355 (t0) cc_final: 0.7793 (t0) REVERT: B 210 SER cc_start: 0.8275 (m) cc_final: 0.7924 (p) REVERT: B 306 ASP cc_start: 0.8740 (t0) cc_final: 0.8381 (t0) REVERT: B 319 MET cc_start: 0.8090 (tpt) cc_final: 0.7748 (tpt) REVERT: B 324 ARG cc_start: 0.5261 (tpt-90) cc_final: 0.4918 (mtp180) REVERT: B 607 ASP cc_start: 0.7697 (t0) cc_final: 0.7477 (m-30) REVERT: B 682 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6166 (tp30) outliers start: 29 outliers final: 16 residues processed: 218 average time/residue: 0.0912 time to fit residues: 28.0252 Evaluate side-chains 215 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.236100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185155 restraints weight = 9425.770| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.06 r_work: 0.3974 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9107 Z= 0.147 Angle : 0.675 12.581 12278 Z= 0.329 Chirality : 0.042 0.218 1370 Planarity : 0.005 0.065 1500 Dihedral : 10.929 59.985 1432 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.68 % Allowed : 16.96 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1046 helix: 0.28 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.65 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.025 0.002 TYR A 305 PHE 0.017 0.001 PHE A 554 TRP 0.019 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9098) covalent geometry : angle 0.67530 / 0.33 (12278) hydrogen bonds : bond 0.03393 / 2.09 ( 429) hydrogen bonds : angle 4.28059 / 2.95 ( 1251) Misc. bond : bond 0.00125 / 0.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8141 (tppt) cc_final: 0.7507 (ttpt) REVERT: A 119 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 137 PHE cc_start: 0.8915 (t80) cc_final: 0.8487 (t80) REVERT: A 142 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 166 ASP cc_start: 0.8309 (t0) cc_final: 0.7784 (t0) REVERT: A 200 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7978 (ttp-170) REVERT: A 210 SER cc_start: 0.8195 (m) cc_final: 0.7851 (p) REVERT: A 213 LEU cc_start: 0.9073 (mm) cc_final: 0.8763 (mm) REVERT: A 272 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 319 MET cc_start: 0.8026 (tpt) cc_final: 0.7701 (tpt) REVERT: A 324 ARG cc_start: 0.5485 (tpt-90) cc_final: 0.5104 (mtp180) REVERT: A 346 GLN cc_start: 0.8457 (pt0) cc_final: 0.8080 (pm20) REVERT: A 660 ILE cc_start: 0.5320 (OUTLIER) cc_final: 0.4655 (tp) REVERT: A 663 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8176 (mt) REVERT: A 673 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 137 PHE cc_start: 0.8925 (t80) cc_final: 0.8518 (t80) REVERT: B 166 ASP cc_start: 0.8324 (t0) cc_final: 0.7831 (t0) REVERT: B 210 SER cc_start: 0.8003 (m) cc_final: 0.7708 (p) REVERT: B 306 ASP cc_start: 0.8595 (t0) cc_final: 0.8371 (t0) REVERT: B 319 MET cc_start: 0.8050 (tpt) cc_final: 0.7709 (tpt) REVERT: B 324 ARG cc_start: 0.5421 (tpt-90) cc_final: 0.5021 (mtp180) REVERT: B 682 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6158 (tp30) outliers start: 24 outliers final: 18 residues processed: 221 average time/residue: 0.0873 time to fit residues: 27.3536 Evaluate side-chains 216 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 618 ASN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.238007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188005 restraints weight = 9354.048| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.02 r_work: 0.4000 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9107 Z= 0.134 Angle : 0.668 11.536 12278 Z= 0.325 Chirality : 0.041 0.168 1370 Planarity : 0.005 0.068 1500 Dihedral : 10.546 59.921 1432 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.23 % Allowed : 17.41 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1046 helix: 0.35 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.034 0.002 TYR A 305 PHE 0.016 0.001 PHE A 554 TRP 0.019 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9098) covalent geometry : angle 0.66792 / 0.33 (12278) hydrogen bonds : bond 0.03268 / 2.00 ( 429) hydrogen bonds : angle 4.20620 / 2.90 ( 1251) Misc. bond : bond 0.00114 / 0.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8048 (tppt) cc_final: 0.7488 (ttpt) REVERT: A 119 GLU cc_start: 0.7769 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 137 PHE cc_start: 0.8804 (t80) cc_final: 0.8376 (t80) REVERT: A 142 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 166 ASP cc_start: 0.8250 (t0) cc_final: 0.7801 (t0) REVERT: A 200 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7940 (ttp-170) REVERT: A 210 SER cc_start: 0.8152 (m) cc_final: 0.7830 (p) REVERT: A 213 LEU cc_start: 0.9062 (mm) cc_final: 0.8788 (mm) REVERT: A 224 MET cc_start: 0.8423 (mtm) cc_final: 0.8216 (mtm) REVERT: A 272 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (mm) REVERT: A 319 MET cc_start: 0.7870 (tpt) cc_final: 0.7598 (tpt) REVERT: A 324 ARG cc_start: 0.5543 (tpt-90) cc_final: 0.5145 (mtp180) REVERT: A 632 TRP cc_start: 0.8633 (p-90) cc_final: 0.7884 (p-90) REVERT: A 660 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4432 (tp) REVERT: A 673 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 69 ARG cc_start: 0.7882 (mmp80) cc_final: 0.7598 (mmp80) REVERT: B 95 LYS cc_start: 0.8060 (tppt) cc_final: 0.7408 (ttpt) REVERT: B 137 PHE cc_start: 0.8862 (t80) cc_final: 0.8470 (t80) REVERT: B 166 ASP cc_start: 0.8287 (t0) cc_final: 0.7838 (t0) REVERT: B 210 SER cc_start: 0.7984 (m) cc_final: 0.7671 (p) REVERT: B 306 ASP cc_start: 0.8453 (t0) cc_final: 0.8220 (t0) REVERT: B 319 MET cc_start: 0.8033 (tpt) cc_final: 0.7681 (tpt) REVERT: B 324 ARG cc_start: 0.5438 (tpt-90) cc_final: 0.5018 (mtp180) REVERT: B 682 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6226 (tp30) outliers start: 20 outliers final: 14 residues processed: 214 average time/residue: 0.0897 time to fit residues: 27.3486 Evaluate side-chains 207 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 77 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 overall best weight: 0.2892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.240796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.190484 restraints weight = 9453.574| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.09 r_work: 0.4041 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9107 Z= 0.125 Angle : 0.662 10.935 12278 Z= 0.321 Chirality : 0.041 0.150 1370 Planarity : 0.004 0.064 1500 Dihedral : 10.063 59.479 1432 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.79 % Allowed : 18.19 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1046 helix: 0.50 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.026 0.002 TYR A 305 PHE 0.023 0.001 PHE B 388 TRP 0.021 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9098) covalent geometry : angle 0.66170 / 0.32 (12278) hydrogen bonds : bond 0.03181 / 1.96 ( 429) hydrogen bonds : angle 4.15048 / 2.86 ( 1251) Misc. bond : bond 0.00102 / 0.05 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7972 (tppt) cc_final: 0.7463 (ttpt) REVERT: A 119 GLU cc_start: 0.7806 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 137 PHE cc_start: 0.8812 (t80) cc_final: 0.8376 (t80) REVERT: A 142 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 151 ARG cc_start: 0.6889 (ttp-170) cc_final: 0.6210 (ptm160) REVERT: A 166 ASP cc_start: 0.8251 (t0) cc_final: 0.7811 (t0) REVERT: A 200 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7933 (ttp-170) REVERT: A 210 SER cc_start: 0.8141 (m) cc_final: 0.7781 (p) REVERT: A 213 LEU cc_start: 0.8993 (mm) cc_final: 0.8712 (mm) REVERT: A 272 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 319 MET cc_start: 0.7833 (tpt) cc_final: 0.7562 (tpt) REVERT: A 324 ARG cc_start: 0.5380 (tpt-90) cc_final: 0.4958 (mtp180) REVERT: A 632 TRP cc_start: 0.8518 (p-90) cc_final: 0.8190 (p-90) REVERT: A 660 ILE cc_start: 0.4851 (OUTLIER) cc_final: 0.4363 (tp) REVERT: A 673 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 95 LYS cc_start: 0.7962 (tppt) cc_final: 0.7334 (ttpt) REVERT: B 137 PHE cc_start: 0.8846 (t80) cc_final: 0.8474 (t80) REVERT: B 166 ASP cc_start: 0.8283 (t0) cc_final: 0.7844 (t0) REVERT: B 210 SER cc_start: 0.8023 (m) cc_final: 0.7510 (p) REVERT: B 306 ASP cc_start: 0.8706 (t0) cc_final: 0.8403 (t0) REVERT: B 319 MET cc_start: 0.8023 (tpt) cc_final: 0.7669 (tpt) REVERT: B 324 ARG cc_start: 0.5309 (tpt-90) cc_final: 0.4885 (mtp180) REVERT: B 335 ASP cc_start: 0.7054 (m-30) cc_final: 0.6074 (t70) REVERT: B 682 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6184 (tp30) outliers start: 16 outliers final: 12 residues processed: 212 average time/residue: 0.0886 time to fit residues: 26.7564 Evaluate side-chains 209 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 0.0270 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.239791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189189 restraints weight = 9321.800| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.07 r_work: 0.4040 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9107 Z= 0.137 Angle : 0.677 11.400 12278 Z= 0.328 Chirality : 0.042 0.146 1370 Planarity : 0.005 0.064 1500 Dihedral : 10.084 59.280 1432 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.90 % Allowed : 18.97 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1046 helix: 0.53 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 69 TYR 0.026 0.002 TYR B 305 PHE 0.020 0.001 PHE A 554 TRP 0.021 0.001 TRP B 92 HIS 0.009 0.003 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9098) covalent geometry : angle 0.67688 / 0.33 (12278) hydrogen bonds : bond 0.03205 / 1.96 ( 429) hydrogen bonds : angle 4.17311 / 2.88 ( 1251) Misc. bond : bond 0.00106 / 0.05 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.44 seconds wall clock time: 44 minutes 43.41 seconds (2683.41 seconds total)