Starting phenix.real_space_refine on Fri Mar 14 00:35:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_8957_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_8957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_8957.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_8957_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1m_8957/03_2025/6e1m_8957_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} 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: 5.88, per 1000 atoms: 0.66 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: 2.61 Conformation dependent library (CDL) restraints added in 999.5 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: 0.86 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: 2.25 Time building geometry restraints manager: 3.01 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: 4623 13.95 - 27.89: 514 27.89 - 41.84: 130 41.84 - 55.78: 67 55.78 - 69.73: 38 Dihedral angle restraints: 5372 sinusoidal: 2210 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 5369 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 707 or resid 801 through 802 or resid 806 throu \ gh 809)) selection = (chain 'B' and (resid 22 through 707 or resid 801 through 802 or resid 806 throu \ gh 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: 1.480 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.450 Find NCS groups from input model: 0.390 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 9098 Z= 1.127 Angle : 1.611 21.272 12278 Z= 0.790 Chirality : 0.079 0.416 1370 Planarity : 0.009 0.073 1500 Dihedral : 14.976 69.726 3328 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.006 TRP B 632 HIS 0.008 0.005 HIS A 27 PHE 0.042 0.006 PHE B 652 TYR 0.058 0.007 TYR A 305 ARG 0.006 0.001 ARG A 700 *********************** 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 : 0.947 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: 0.8079 (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: 0.2173 time to fit residues: 85.4188 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 : 0.920 ------------------------------------------------------------------------------- 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 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.0000 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 257 GLN B 585 GLN B 618 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.231325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178957 restraints weight = 9271.956| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.32 r_work: 0.3903 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9098 Z= 0.239 Angle : 0.786 11.760 12278 Z= 0.403 Chirality : 0.044 0.198 1370 Planarity : 0.006 0.064 1500 Dihedral : 15.022 59.628 1452 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.90 % Allowed : 8.93 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.22), residues: 1046 helix: -2.18 (0.16), residues: 720 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.024 0.002 PHE B 67 TYR 0.025 0.003 TYR A 141 ARG 0.008 0.001 ARG B 200 *********************** 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: 17 poor density : 243 time to evaluate : 0.842 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: 0.6859 (t70) cc_final: 0.6629 (t70) REVERT: A 115 LEU cc_start: 0.8219 (mt) cc_final: 0.7822 (mt) REVERT: A 119 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6858 (tm-30) REVERT: A 166 ASP cc_start: 0.8156 (t0) cc_final: 0.7504 (t0) REVERT: A 200 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7936 (ttp-170) REVERT: A 210 SER cc_start: 0.8572 (m) cc_final: 0.8074 (p) REVERT: A 319 MET cc_start: 0.8392 (tpt) cc_final: 0.7874 (tpt) REVERT: A 550 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.6498 (ttm-80) REVERT: A 607 ASP cc_start: 0.8286 (t70) cc_final: 0.7875 (m-30) REVERT: A 626 LEU cc_start: 0.9129 (mt) cc_final: 0.8893 (mp) REVERT: A 634 VAL cc_start: 0.8984 (t) cc_final: 0.8646 (m) REVERT: A 656 TYR cc_start: 0.8669 (t80) cc_final: 0.8095 (t80) REVERT: A 660 ILE cc_start: 0.6068 (mm) cc_final: 0.5765 (tp) REVERT: A 676 PHE cc_start: 0.7641 (m-10) cc_final: 0.7208 (m-10) REVERT: A 677 THR cc_start: 0.7082 (m) cc_final: 0.6621 (p) REVERT: A 678 GLU cc_start: 0.6637 (mp0) cc_final: 0.5998 (mp0) REVERT: A 682 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6292 (tp30) REVERT: B 115 LEU cc_start: 0.8029 (mt) cc_final: 0.7683 (mt) REVERT: B 166 ASP cc_start: 0.8174 (t0) cc_final: 0.7601 (t0) REVERT: B 200 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7883 (ttp-170) REVERT: B 210 SER cc_start: 0.8594 (m) cc_final: 0.8191 (p) REVERT: B 319 MET cc_start: 0.8277 (tpt) cc_final: 0.7854 (tpt) REVERT: B 324 ARG cc_start: 0.5601 (tpt-90) cc_final: 0.5375 (mmm160) REVERT: B 338 LYS cc_start: 0.8819 (mttt) cc_final: 0.7620 (tptt) REVERT: B 607 ASP cc_start: 0.8318 (t0) cc_final: 0.7978 (t0) REVERT: B 673 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 677 THR cc_start: 0.7240 (m) cc_final: 0.6888 (p) outliers start: 17 outliers final: 9 residues processed: 256 average time/residue: 0.2084 time to fit residues: 73.0048 Evaluate side-chains 220 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 B residue 101 CYS 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 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 134 HIS ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 134 HIS B 585 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.234686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.182361 restraints weight = 9496.967| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.25 r_work: 0.3936 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9098 Z= 0.232 Angle : 0.711 10.482 12278 Z= 0.358 Chirality : 0.042 0.158 1370 Planarity : 0.005 0.069 1500 Dihedral : 13.424 61.834 1452 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.23 % Allowed : 11.27 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.24), residues: 1046 helix: -1.26 (0.17), residues: 732 sheet: None (None), residues: 0 loop : -2.20 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.018 0.002 PHE B 624 TYR 0.021 0.002 TYR B 256 ARG 0.005 0.000 ARG B 200 *********************** 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 247 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.886 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: 0.8555 (pptt) cc_final: 0.8235 (ptpp) REVERT: A 96 ASN cc_start: 0.8039 (p0) cc_final: 0.7672 (p0) REVERT: A 115 LEU cc_start: 0.8154 (mt) cc_final: 0.7754 (mt) REVERT: A 119 GLU cc_start: 0.7911 (mm-30) cc_final: 0.6972 (tm-30) REVERT: A 166 ASP cc_start: 0.8217 (t0) cc_final: 0.7607 (t0) REVERT: A 200 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7925 (ttp-170) REVERT: A 210 SER cc_start: 0.8604 (m) cc_final: 0.8113 (p) REVERT: A 279 ARG cc_start: 0.9029 (mmt-90) cc_final: 0.6813 (mmt180) REVERT: A 319 MET cc_start: 0.8320 (tpt) cc_final: 0.7947 (tpt) REVERT: A 388 PHE cc_start: 0.7876 (t80) cc_final: 0.7409 (t80) REVERT: A 626 LEU cc_start: 0.9025 (mt) cc_final: 0.8823 (mp) REVERT: A 634 VAL cc_start: 0.8897 (t) cc_final: 0.8643 (m) REVERT: A 656 TYR cc_start: 0.8779 (t80) cc_final: 0.8182 (t80) REVERT: A 677 THR cc_start: 0.7178 (m) cc_final: 0.6751 (p) REVERT: A 682 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6408 (tp30) REVERT: B 96 ASN cc_start: 0.7911 (p0) cc_final: 0.7447 (p0) REVERT: B 115 LEU cc_start: 0.7902 (mt) cc_final: 0.7586 (mt) REVERT: B 137 PHE cc_start: 0.8857 (t80) cc_final: 0.8330 (t80) REVERT: B 141 TYR cc_start: 0.8748 (p90) cc_final: 0.8512 (p90) REVERT: B 146 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8170 (tp) REVERT: B 166 ASP cc_start: 0.8245 (t0) cc_final: 0.7724 (t0) REVERT: B 210 SER cc_start: 0.8672 (m) cc_final: 0.8290 (p) REVERT: B 319 MET cc_start: 0.8309 (tpt) cc_final: 0.7885 (tpt) REVERT: B 324 ARG cc_start: 0.5484 (tpt-90) cc_final: 0.4944 (mtp180) REVERT: B 338 LYS cc_start: 0.8784 (mttt) cc_final: 0.7636 (tptt) REVERT: B 386 ASP cc_start: 0.7945 (t0) cc_final: 0.7699 (t0) REVERT: B 387 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7518 (mp0) REVERT: B 607 ASP cc_start: 0.8050 (t0) cc_final: 0.7475 (m-30) REVERT: B 663 LEU cc_start: 0.8703 (mt) cc_final: 0.8409 (mt) REVERT: B 673 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 677 THR cc_start: 0.7379 (m) cc_final: 0.6989 (p) REVERT: B 682 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6063 (tp30) outliers start: 20 outliers final: 14 residues processed: 240 average time/residue: 0.2032 time to fit residues: 67.6227 Evaluate side-chains 222 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 146 ILE 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 658 ILE 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 17 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.234977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183447 restraints weight = 9355.576| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.21 r_work: 0.3956 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9098 Z= 0.202 Angle : 0.675 8.909 12278 Z= 0.336 Chirality : 0.041 0.172 1370 Planarity : 0.004 0.066 1500 Dihedral : 12.528 63.426 1452 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.01 % Allowed : 13.95 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1046 helix: -0.70 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -2.04 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.029 0.001 PHE A 65 TYR 0.021 0.002 TYR B 216 ARG 0.002 0.000 ARG A 104 *********************** 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: 27 poor density : 216 time to evaluate : 0.863 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: 0.8512 (pptt) cc_final: 0.8290 (ptpp) REVERT: A 96 ASN cc_start: 0.8029 (p0) cc_final: 0.7648 (p0) REVERT: A 115 LEU cc_start: 0.8161 (mt) cc_final: 0.7769 (mt) REVERT: A 119 GLU cc_start: 0.7892 (mm-30) cc_final: 0.6865 (tm-30) REVERT: A 137 PHE cc_start: 0.8890 (t80) cc_final: 0.8555 (t80) REVERT: A 166 ASP cc_start: 0.8153 (t0) cc_final: 0.7685 (t0) REVERT: A 200 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7952 (ttp-170) REVERT: A 210 SER cc_start: 0.8086 (m) cc_final: 0.7657 (p) REVERT: A 319 MET cc_start: 0.8211 (tpt) cc_final: 0.7805 (tpt) REVERT: A 388 PHE cc_start: 0.7967 (t80) cc_final: 0.7614 (t80) REVERT: A 637 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7197 (tm-30) REVERT: A 656 TYR cc_start: 0.8732 (t80) cc_final: 0.8496 (t80) REVERT: A 682 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6375 (tp30) REVERT: B 95 LYS cc_start: 0.8163 (tppt) cc_final: 0.7770 (ttpt) REVERT: B 96 ASN cc_start: 0.7936 (p0) cc_final: 0.7520 (p0) REVERT: B 115 LEU cc_start: 0.8004 (mt) cc_final: 0.7716 (mt) REVERT: B 137 PHE cc_start: 0.8845 (t80) cc_final: 0.8379 (t80) REVERT: B 166 ASP cc_start: 0.8177 (t0) cc_final: 0.7701 (t0) REVERT: B 210 SER cc_start: 0.8149 (m) cc_final: 0.7809 (p) REVERT: B 319 MET cc_start: 0.8174 (tpt) cc_final: 0.7775 (tpt) REVERT: B 324 ARG cc_start: 0.5363 (tpt-90) cc_final: 0.5032 (mtp180) REVERT: B 338 LYS cc_start: 0.8730 (mttt) cc_final: 0.7579 (tptt) REVERT: B 607 ASP cc_start: 0.7946 (t0) cc_final: 0.7579 (m-30) REVERT: B 663 LEU cc_start: 0.8465 (mt) cc_final: 0.8160 (mt) REVERT: B 677 THR cc_start: 0.7389 (m) cc_final: 0.6963 (p) REVERT: B 682 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6296 (tp30) outliers start: 27 outliers final: 18 residues processed: 229 average time/residue: 0.2074 time to fit residues: 65.8627 Evaluate side-chains 216 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 168 LEU 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 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 215 THR Chi-restraints excluded: chain B residue 233 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 105 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4611 r_free = 0.4611 target = 0.235792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183828 restraints weight = 9288.588| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.21 r_work: 0.3971 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9098 Z= 0.198 Angle : 0.674 11.350 12278 Z= 0.333 Chirality : 0.041 0.144 1370 Planarity : 0.004 0.066 1500 Dihedral : 12.073 63.084 1452 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.01 % Allowed : 14.73 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1046 helix: -0.27 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.027 0.001 PHE A 65 TYR 0.024 0.002 TYR B 107 ARG 0.002 0.000 ARG A 104 *********************** 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 226 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.817 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: A 95 LYS cc_start: 0.8178 (tppt) cc_final: 0.7764 (ttpt) REVERT: A 115 LEU cc_start: 0.8125 (mt) cc_final: 0.7698 (mt) REVERT: A 119 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7093 (tm-30) REVERT: A 137 PHE cc_start: 0.8877 (t80) cc_final: 0.8433 (t80) REVERT: A 166 ASP cc_start: 0.8122 (t0) cc_final: 0.7663 (t0) REVERT: A 200 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7940 (ttp-170) REVERT: A 210 SER cc_start: 0.8079 (m) cc_final: 0.7724 (p) REVERT: A 319 MET cc_start: 0.8126 (tpt) cc_final: 0.7727 (tpt) REVERT: A 388 PHE cc_start: 0.8002 (t80) cc_final: 0.7637 (t80) REVERT: A 634 VAL cc_start: 0.8942 (t) cc_final: 0.8680 (m) REVERT: A 637 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 656 TYR cc_start: 0.8733 (t80) cc_final: 0.8533 (t80) REVERT: A 659 THR cc_start: 0.7810 (m) cc_final: 0.7497 (p) REVERT: A 660 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.5230 (tp) REVERT: A 682 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6397 (tp30) REVERT: B 96 ASN cc_start: 0.7857 (p0) cc_final: 0.7468 (p0) REVERT: B 107 TYR cc_start: 0.5808 (p90) cc_final: 0.5087 (m-10) REVERT: B 115 LEU cc_start: 0.7947 (mt) cc_final: 0.7659 (mt) REVERT: B 137 PHE cc_start: 0.8879 (t80) cc_final: 0.8433 (t80) REVERT: B 166 ASP cc_start: 0.8215 (t0) cc_final: 0.7741 (t0) REVERT: B 210 SER cc_start: 0.8171 (m) cc_final: 0.7875 (p) REVERT: B 319 MET cc_start: 0.8142 (tpt) cc_final: 0.7777 (tpt) REVERT: B 324 ARG cc_start: 0.5319 (tpt-90) cc_final: 0.4977 (mtp180) REVERT: B 338 LYS cc_start: 0.8694 (mttt) cc_final: 0.7536 (tptp) REVERT: B 341 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7448 (mm-30) REVERT: B 607 ASP cc_start: 0.7861 (t0) cc_final: 0.7555 (m-30) REVERT: B 677 THR cc_start: 0.7441 (m) cc_final: 0.7038 (p) REVERT: B 682 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6241 (tp30) outliers start: 27 outliers final: 16 residues processed: 215 average time/residue: 0.2027 time to fit residues: 60.3838 Evaluate side-chains 208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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 186 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 585 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.236140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183674 restraints weight = 9378.568| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.10 r_work: 0.3971 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9098 Z= 0.203 Angle : 0.670 9.669 12278 Z= 0.330 Chirality : 0.041 0.143 1370 Planarity : 0.004 0.065 1500 Dihedral : 11.668 64.182 1452 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.24 % Allowed : 15.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1046 helix: 0.08 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.019 0.001 PHE B 388 TYR 0.034 0.002 TYR A 305 ARG 0.003 0.000 ARG A 104 *********************** 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 236 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8621 (pptt) cc_final: 0.8248 (ptpp) REVERT: A 115 LEU cc_start: 0.8147 (mt) cc_final: 0.7700 (mt) REVERT: A 119 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7087 (tm-30) REVERT: A 137 PHE cc_start: 0.8911 (t80) cc_final: 0.8475 (t80) REVERT: A 151 ARG cc_start: 0.7019 (ttp-170) cc_final: 0.6298 (ptm160) REVERT: A 166 ASP cc_start: 0.8349 (t0) cc_final: 0.7746 (t0) REVERT: A 200 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7901 (ttp-170) REVERT: A 210 SER cc_start: 0.8201 (m) cc_final: 0.7763 (p) REVERT: A 319 MET cc_start: 0.8118 (tpt) cc_final: 0.7750 (tpt) REVERT: A 637 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 659 THR cc_start: 0.7663 (m) cc_final: 0.7278 (p) REVERT: A 660 ILE cc_start: 0.5540 (OUTLIER) cc_final: 0.5073 (tp) REVERT: B 96 ASN cc_start: 0.7851 (p0) cc_final: 0.7514 (p0) REVERT: B 137 PHE cc_start: 0.8862 (t80) cc_final: 0.8439 (t80) REVERT: B 166 ASP cc_start: 0.8378 (t0) cc_final: 0.7795 (t0) REVERT: B 210 SER cc_start: 0.8259 (m) cc_final: 0.7913 (p) REVERT: B 262 PHE cc_start: 0.8791 (t80) cc_final: 0.8414 (t80) REVERT: B 319 MET cc_start: 0.8073 (tpt) cc_final: 0.7734 (tpt) REVERT: B 324 ARG cc_start: 0.5352 (tpt-90) cc_final: 0.5010 (mtp180) REVERT: B 338 LYS cc_start: 0.8658 (mttt) cc_final: 0.7542 (tptp) REVERT: B 341 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7388 (mm-30) REVERT: B 607 ASP cc_start: 0.7806 (t0) cc_final: 0.7595 (m-30) REVERT: B 663 LEU cc_start: 0.9043 (mm) cc_final: 0.8832 (mt) REVERT: B 682 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6239 (tp30) outliers start: 29 outliers final: 20 residues processed: 222 average time/residue: 0.1845 time to fit residues: 57.5467 Evaluate side-chains 215 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4601 r_free = 0.4601 target = 0.234591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.184657 restraints weight = 9388.604| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.15 r_work: 0.3963 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9098 Z= 0.249 Angle : 0.685 9.348 12278 Z= 0.337 Chirality : 0.042 0.157 1370 Planarity : 0.005 0.070 1500 Dihedral : 11.687 63.738 1452 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.12 % Allowed : 16.96 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1046 helix: 0.19 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.018 0.001 PHE B 554 TYR 0.030 0.002 TYR A 305 ARG 0.002 0.000 ARG A 279 *********************** 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 229 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.022 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: 0.8575 (pptt) cc_final: 0.8230 (ptpp) REVERT: A 95 LYS cc_start: 0.8074 (tppt) cc_final: 0.7536 (ttpt) REVERT: A 115 LEU cc_start: 0.8166 (mt) cc_final: 0.7719 (mt) REVERT: A 119 GLU cc_start: 0.7897 (mm-30) cc_final: 0.6827 (tm-30) REVERT: A 137 PHE cc_start: 0.8912 (t80) cc_final: 0.8475 (t80) REVERT: A 151 ARG cc_start: 0.6989 (ttp-170) cc_final: 0.6302 (ptm160) REVERT: A 166 ASP cc_start: 0.8301 (t0) cc_final: 0.7744 (t0) REVERT: A 200 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7979 (ttp-170) REVERT: A 210 SER cc_start: 0.8232 (m) cc_final: 0.7898 (p) REVERT: A 213 LEU cc_start: 0.9124 (mm) cc_final: 0.8841 (mm) REVERT: A 319 MET cc_start: 0.8030 (tpt) cc_final: 0.7696 (tpt) REVERT: A 634 VAL cc_start: 0.8972 (t) cc_final: 0.8690 (m) REVERT: A 660 ILE cc_start: 0.5278 (OUTLIER) cc_final: 0.4552 (tp) REVERT: B 96 ASN cc_start: 0.7864 (p0) cc_final: 0.7563 (p0) REVERT: B 137 PHE cc_start: 0.8868 (t80) cc_final: 0.8450 (t80) REVERT: B 166 ASP cc_start: 0.8349 (t0) cc_final: 0.7819 (t0) REVERT: B 210 SER cc_start: 0.8062 (m) cc_final: 0.7758 (p) REVERT: B 262 PHE cc_start: 0.8788 (t80) cc_final: 0.8400 (t80) REVERT: B 319 MET cc_start: 0.8018 (tpt) cc_final: 0.7682 (tpt) REVERT: B 324 ARG cc_start: 0.5409 (tpt-90) cc_final: 0.4966 (mtp180) REVERT: B 338 LYS cc_start: 0.8660 (mttt) cc_final: 0.7547 (tptp) REVERT: B 341 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7406 (tp30) REVERT: B 607 ASP cc_start: 0.7748 (t0) cc_final: 0.7503 (m-30) REVERT: B 663 LEU cc_start: 0.9096 (mm) cc_final: 0.8877 (mt) REVERT: B 682 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6044 (tp30) outliers start: 28 outliers final: 19 residues processed: 216 average time/residue: 0.2147 time to fit residues: 64.9450 Evaluate side-chains 213 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 168 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 86 optimal weight: 0.0470 chunk 95 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4624 r_free = 0.4624 target = 0.237819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187112 restraints weight = 9506.926| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.11 r_work: 0.4004 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9098 Z= 0.189 Angle : 0.670 14.763 12278 Z= 0.326 Chirality : 0.041 0.157 1370 Planarity : 0.004 0.067 1500 Dihedral : 11.106 65.373 1452 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.34 % Allowed : 17.75 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1046 helix: 0.35 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.015 0.001 PHE B 554 TYR 0.025 0.002 TYR A 305 ARG 0.002 0.000 ARG A 151 *********************** 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 232 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.239 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: A 33 LYS cc_start: 0.8471 (pptt) cc_final: 0.8186 (ptpp) REVERT: A 95 LYS cc_start: 0.7963 (tppt) cc_final: 0.7531 (ttpt) REVERT: A 119 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 137 PHE cc_start: 0.8841 (t80) cc_final: 0.8404 (t80) REVERT: A 142 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 151 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.6148 (ptm160) REVERT: A 166 ASP cc_start: 0.8254 (t0) cc_final: 0.7777 (t0) REVERT: A 200 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7948 (ttp-170) REVERT: A 210 SER cc_start: 0.8187 (m) cc_final: 0.7816 (p) REVERT: A 213 LEU cc_start: 0.8992 (mm) cc_final: 0.8675 (mm) REVERT: A 319 MET cc_start: 0.8019 (tpt) cc_final: 0.7744 (tpt) REVERT: A 634 VAL cc_start: 0.8957 (t) cc_final: 0.8693 (m) REVERT: A 660 ILE cc_start: 0.4853 (OUTLIER) cc_final: 0.4209 (tp) REVERT: B 96 ASN cc_start: 0.7851 (p0) cc_final: 0.7593 (p0) REVERT: B 137 PHE cc_start: 0.8790 (t80) cc_final: 0.8377 (t80) REVERT: B 166 ASP cc_start: 0.8289 (t0) cc_final: 0.7813 (t0) REVERT: B 210 SER cc_start: 0.8199 (m) cc_final: 0.7871 (p) REVERT: B 262 PHE cc_start: 0.8771 (t80) cc_final: 0.8429 (t80) REVERT: B 290 LEU cc_start: 0.8830 (tp) cc_final: 0.8552 (mt) REVERT: B 319 MET cc_start: 0.7997 (tpt) cc_final: 0.7621 (tpt) REVERT: B 324 ARG cc_start: 0.5411 (tpt-90) cc_final: 0.5000 (mtp180) REVERT: B 338 LYS cc_start: 0.8713 (mttt) cc_final: 0.7602 (tptp) REVERT: B 341 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7443 (tp30) REVERT: B 663 LEU cc_start: 0.9087 (mm) cc_final: 0.8854 (mp) REVERT: B 682 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6125 (tp30) outliers start: 21 outliers final: 15 residues processed: 224 average time/residue: 0.2435 time to fit residues: 78.2620 Evaluate side-chains 212 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR 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 101 CYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 346 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.238603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.188212 restraints weight = 9428.959| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.04 r_work: 0.4020 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9098 Z= 0.199 Angle : 0.668 13.711 12278 Z= 0.326 Chirality : 0.041 0.153 1370 Planarity : 0.005 0.065 1500 Dihedral : 10.631 59.791 1450 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.12 % Allowed : 18.42 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1046 helix: 0.49 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.022 0.001 PHE B 554 TYR 0.038 0.002 TYR A 305 ARG 0.002 0.000 ARG B 279 *********************** 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: 19 poor density : 201 time to evaluate : 0.848 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: 0.7886 (tppt) cc_final: 0.7488 (ttpt) REVERT: A 119 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7009 (mm-30) REVERT: A 137 PHE cc_start: 0.8838 (t80) cc_final: 0.8421 (t80) REVERT: A 142 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8073 (mt-10) REVERT: A 151 ARG cc_start: 0.6877 (ttp-170) cc_final: 0.6297 (ptm160) REVERT: A 166 ASP cc_start: 0.8186 (t0) cc_final: 0.7767 (t0) REVERT: A 200 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7949 (ttp-170) REVERT: A 210 SER cc_start: 0.8159 (m) cc_final: 0.7818 (p) REVERT: A 213 LEU cc_start: 0.8940 (mm) cc_final: 0.8626 (mm) REVERT: A 319 MET cc_start: 0.7869 (tpt) cc_final: 0.7642 (tpt) REVERT: A 634 VAL cc_start: 0.8924 (t) cc_final: 0.8662 (m) REVERT: A 660 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.4101 (tp) REVERT: B 96 ASN cc_start: 0.7810 (p0) cc_final: 0.7567 (p0) REVERT: B 137 PHE cc_start: 0.8792 (t80) cc_final: 0.8433 (t80) REVERT: B 166 ASP cc_start: 0.8218 (t0) cc_final: 0.7798 (t0) REVERT: B 210 SER cc_start: 0.7993 (m) cc_final: 0.7553 (p) REVERT: B 262 PHE cc_start: 0.8773 (t80) cc_final: 0.8415 (t80) REVERT: B 319 MET cc_start: 0.7978 (tpt) cc_final: 0.7646 (tpt) REVERT: B 324 ARG cc_start: 0.5371 (tpt-90) cc_final: 0.4957 (mtp180) REVERT: B 338 LYS cc_start: 0.8634 (mttt) cc_final: 0.7556 (tptp) REVERT: B 341 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7461 (tp30) REVERT: B 663 LEU cc_start: 0.9113 (mm) cc_final: 0.8881 (mt) REVERT: B 682 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6218 (tp30) outliers start: 19 outliers final: 15 residues processed: 213 average time/residue: 0.1975 time to fit residues: 58.7778 Evaluate side-chains 210 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 168 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4622 r_free = 0.4622 target = 0.237446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186138 restraints weight = 9374.967| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.07 r_work: 0.3992 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9098 Z= 0.230 Angle : 0.695 13.492 12278 Z= 0.338 Chirality : 0.042 0.167 1370 Planarity : 0.005 0.065 1500 Dihedral : 10.754 59.883 1450 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.12 % Allowed : 18.53 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1046 helix: 0.50 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 92 HIS 0.008 0.003 HIS A 27 PHE 0.019 0.001 PHE B 554 TYR 0.035 0.002 TYR A 305 ARG 0.006 0.000 ARG B 69 ********************** 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 215 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7854 (tppt) cc_final: 0.7485 (ttpt) REVERT: A 119 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 137 PHE cc_start: 0.8833 (t80) cc_final: 0.8389 (t80) REVERT: A 142 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 166 ASP cc_start: 0.8313 (t0) cc_final: 0.7819 (t0) REVERT: A 200 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7936 (ttp-170) REVERT: A 210 SER cc_start: 0.8139 (m) cc_final: 0.7735 (p) REVERT: A 213 LEU cc_start: 0.8938 (mm) cc_final: 0.8631 (mm) REVERT: A 319 MET cc_start: 0.8007 (tpt) cc_final: 0.7761 (tpt) REVERT: A 634 VAL cc_start: 0.8951 (t) cc_final: 0.8669 (m) REVERT: A 660 ILE cc_start: 0.4309 (OUTLIER) cc_final: 0.3776 (tp) REVERT: B 67 PHE cc_start: 0.7506 (m-80) cc_final: 0.6995 (m-80) REVERT: B 96 ASN cc_start: 0.7891 (p0) cc_final: 0.7658 (p0) REVERT: B 137 PHE cc_start: 0.8785 (t80) cc_final: 0.8385 (t80) REVERT: B 166 ASP cc_start: 0.8325 (t0) cc_final: 0.7824 (t0) REVERT: B 210 SER cc_start: 0.8111 (m) cc_final: 0.7840 (p) REVERT: B 262 PHE cc_start: 0.8783 (t80) cc_final: 0.8435 (t80) REVERT: B 319 MET cc_start: 0.7996 (tpt) cc_final: 0.7632 (tpt) REVERT: B 324 ARG cc_start: 0.5237 (tpt-90) cc_final: 0.4999 (mtp180) REVERT: B 338 LYS cc_start: 0.8633 (mttt) cc_final: 0.7544 (tptp) REVERT: B 341 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7493 (tp30) REVERT: B 663 LEU cc_start: 0.9119 (mm) cc_final: 0.8879 (mt) REVERT: B 682 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6265 (tm-30) outliers start: 19 outliers final: 16 residues processed: 210 average time/residue: 0.1905 time to fit residues: 56.1587 Evaluate side-chains 208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 168 LEU 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 272 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 ILE 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 650 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.236946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186241 restraints weight = 9355.082| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.98 r_work: 0.4000 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9098 Z= 0.235 Angle : 0.697 13.090 12278 Z= 0.339 Chirality : 0.043 0.213 1370 Planarity : 0.005 0.065 1500 Dihedral : 10.815 59.957 1450 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.23 % Allowed : 18.30 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1046 helix: 0.50 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 92 HIS 0.008 0.003 HIS A 27 PHE 0.020 0.001 PHE B 388 TYR 0.037 0.002 TYR A 305 ARG 0.004 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.83 seconds wall clock time: 98 minutes 10.15 seconds (5890.15 seconds total)