Starting phenix.real_space_refine on Wed Sep 25 03:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_8957_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_8957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_8957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_8957_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/09_2024/6e1m_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-5461/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: 5.95, per 1000 atoms: 0.67 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 958.2 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: 0.97 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: 2.44 Time building geometry restraints manager: 2.88 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: 2.390 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 0.892 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: 0.2090 time to fit residues: 82.3624 Evaluate side-chains 211 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 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 fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 0.959 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: 0.6938 (t70) cc_final: 0.6679 (t70) REVERT: A 115 LEU cc_start: 0.8154 (mt) cc_final: 0.7788 (mt) REVERT: A 119 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6806 (tm-30) REVERT: A 166 ASP cc_start: 0.8075 (t0) cc_final: 0.7414 (t0) REVERT: A 200 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7671 (ttp-170) REVERT: A 210 SER cc_start: 0.8508 (m) cc_final: 0.8002 (p) REVERT: A 319 MET cc_start: 0.8082 (tpt) cc_final: 0.7524 (tpt) REVERT: A 550 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.6409 (ttm-80) REVERT: A 607 ASP cc_start: 0.8024 (t70) cc_final: 0.7639 (m-30) REVERT: A 626 LEU cc_start: 0.8970 (mt) cc_final: 0.8730 (mp) REVERT: A 634 VAL cc_start: 0.8953 (t) cc_final: 0.8558 (m) REVERT: A 656 TYR cc_start: 0.8399 (t80) cc_final: 0.7849 (t80) REVERT: A 658 ILE cc_start: 0.8043 (mt) cc_final: 0.7837 (mm) REVERT: A 676 PHE cc_start: 0.7288 (m-10) cc_final: 0.6873 (m-10) REVERT: A 677 THR cc_start: 0.6900 (m) cc_final: 0.6478 (p) REVERT: A 678 GLU cc_start: 0.6655 (mp0) cc_final: 0.5992 (mp0) REVERT: A 682 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6251 (tp30) REVERT: B 115 LEU cc_start: 0.8020 (mt) cc_final: 0.7698 (mt) REVERT: B 166 ASP cc_start: 0.8024 (t0) cc_final: 0.7478 (t0) REVERT: B 200 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7579 (ttp-170) REVERT: B 210 SER cc_start: 0.8497 (m) cc_final: 0.8082 (p) REVERT: B 319 MET cc_start: 0.8026 (tpt) cc_final: 0.7560 (tpt) REVERT: B 324 ARG cc_start: 0.5323 (tpt-90) cc_final: 0.5122 (mmm160) REVERT: B 338 LYS cc_start: 0.8766 (mttt) cc_final: 0.7605 (tptt) REVERT: B 607 ASP cc_start: 0.8084 (t0) cc_final: 0.7744 (t0) REVERT: B 677 THR cc_start: 0.7048 (m) cc_final: 0.6724 (p) outliers start: 17 outliers final: 9 residues processed: 256 average time/residue: 0.2074 time to fit residues: 72.5220 Evaluate side-chains 220 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 53 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 32 optimal weight: 0.0270 chunk 77 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 257 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 134 HIS B 585 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9098 Z= 0.192 Angle : 0.689 10.455 12278 Z= 0.347 Chirality : 0.041 0.163 1370 Planarity : 0.005 0.069 1500 Dihedral : 13.111 60.494 1452 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.90 % Allowed : 11.16 % Favored : 86.94 % 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: -2.45 (0.24), residues: 1046 helix: -1.23 (0.17), residues: 732 sheet: None (None), residues: 0 loop : -2.24 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 92 HIS 0.007 0.001 HIS B 27 PHE 0.018 0.001 PHE B 624 TYR 0.021 0.002 TYR B 216 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 249 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 0.943 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 27 HIS cc_start: 0.6993 (t70) cc_final: 0.6779 (t70) REVERT: A 33 LYS cc_start: 0.8723 (pptt) cc_final: 0.8357 (ptpp) REVERT: A 96 ASN cc_start: 0.7959 (p0) cc_final: 0.7576 (p0) REVERT: A 115 LEU cc_start: 0.8047 (mt) cc_final: 0.7695 (mt) REVERT: A 119 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6855 (tm-30) REVERT: A 166 ASP cc_start: 0.8167 (t0) cc_final: 0.7602 (t0) REVERT: A 200 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7629 (ttp-170) REVERT: A 210 SER cc_start: 0.8456 (m) cc_final: 0.7977 (p) REVERT: A 279 ARG cc_start: 0.8814 (mmt-90) cc_final: 0.6711 (mmt180) REVERT: A 290 LEU cc_start: 0.8895 (tp) cc_final: 0.8663 (mt) REVERT: A 319 MET cc_start: 0.7914 (tpt) cc_final: 0.7516 (tpt) REVERT: A 388 PHE cc_start: 0.7826 (t80) cc_final: 0.7401 (t80) REVERT: A 634 VAL cc_start: 0.8827 (t) cc_final: 0.8476 (m) REVERT: A 663 LEU cc_start: 0.8370 (mt) cc_final: 0.8142 (mt) REVERT: A 676 PHE cc_start: 0.7378 (m-10) cc_final: 0.7099 (m-10) REVERT: A 677 THR cc_start: 0.6788 (m) cc_final: 0.6416 (p) REVERT: A 682 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6316 (tp30) REVERT: B 96 ASN cc_start: 0.7797 (p0) cc_final: 0.7339 (p0) REVERT: B 115 LEU cc_start: 0.7823 (mt) cc_final: 0.7541 (mt) REVERT: B 137 PHE cc_start: 0.8722 (t80) cc_final: 0.8128 (t80) REVERT: B 141 TYR cc_start: 0.8589 (p90) cc_final: 0.8334 (p90) REVERT: B 166 ASP cc_start: 0.8117 (t0) cc_final: 0.7611 (t0) REVERT: B 210 SER cc_start: 0.8538 (m) cc_final: 0.8093 (p) REVERT: B 290 LEU cc_start: 0.8781 (tp) cc_final: 0.8490 (mt) REVERT: B 319 MET cc_start: 0.7900 (tpt) cc_final: 0.7449 (tpt) REVERT: B 324 ARG cc_start: 0.5115 (tpt-90) cc_final: 0.4627 (mtp180) REVERT: B 338 LYS cc_start: 0.8729 (mttt) cc_final: 0.7613 (tptt) REVERT: B 387 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8190 (mp0) REVERT: B 607 ASP cc_start: 0.7839 (t0) cc_final: 0.7281 (m-30) REVERT: B 663 LEU cc_start: 0.8241 (mt) cc_final: 0.7909 (mt) REVERT: B 677 THR cc_start: 0.7110 (m) cc_final: 0.6783 (p) REVERT: B 682 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6115 (tp30) outliers start: 17 outliers final: 13 residues processed: 243 average time/residue: 0.2049 time to fit residues: 68.8878 Evaluate side-chains 222 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 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 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 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 346 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9098 Z= 0.254 Angle : 0.707 9.036 12278 Z= 0.350 Chirality : 0.043 0.196 1370 Planarity : 0.005 0.066 1500 Dihedral : 12.728 63.427 1452 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.24 % Allowed : 13.62 % Favored : 83.15 % 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: -1.78 (0.25), residues: 1046 helix: -0.72 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -2.03 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.008 0.002 HIS B 27 PHE 0.028 0.002 PHE A 65 TYR 0.020 0.002 TYR B 216 ARG 0.003 0.000 ARG A 279 *********************** 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 237 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 1.038 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: 0.7021 (t70) cc_final: 0.6784 (t70) REVERT: A 33 LYS cc_start: 0.8710 (pptt) cc_final: 0.8350 (ptpp) REVERT: A 115 LEU cc_start: 0.8067 (mt) cc_final: 0.7690 (mt) REVERT: A 119 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6771 (tm-30) REVERT: A 137 PHE cc_start: 0.8780 (t80) cc_final: 0.8373 (t80) REVERT: A 166 ASP cc_start: 0.8150 (t0) cc_final: 0.7604 (t0) REVERT: A 200 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7658 (ttp-170) REVERT: A 210 SER cc_start: 0.7993 (m) cc_final: 0.7564 (p) REVERT: A 290 LEU cc_start: 0.8832 (tp) cc_final: 0.8429 (mt) REVERT: A 319 MET cc_start: 0.7905 (tpt) cc_final: 0.7442 (tpt) REVERT: A 388 PHE cc_start: 0.7826 (t80) cc_final: 0.7431 (t80) REVERT: A 634 VAL cc_start: 0.8894 (t) cc_final: 0.8562 (m) REVERT: A 682 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6278 (tp30) REVERT: B 96 ASN cc_start: 0.7957 (p0) cc_final: 0.7587 (p0) REVERT: B 115 LEU cc_start: 0.7951 (mt) cc_final: 0.7693 (mt) REVERT: B 137 PHE cc_start: 0.8757 (t80) cc_final: 0.8202 (t80) REVERT: B 166 ASP cc_start: 0.8112 (t0) cc_final: 0.7657 (t0) REVERT: B 210 SER cc_start: 0.8057 (m) cc_final: 0.7651 (p) REVERT: B 290 LEU cc_start: 0.8808 (tp) cc_final: 0.8438 (mt) REVERT: B 319 MET cc_start: 0.7889 (tpt) cc_final: 0.7450 (tpt) REVERT: B 324 ARG cc_start: 0.5103 (tpt-90) cc_final: 0.4809 (mtp180) REVERT: B 338 LYS cc_start: 0.8690 (mttt) cc_final: 0.7579 (tptp) REVERT: B 607 ASP cc_start: 0.7784 (t0) cc_final: 0.7387 (m-30) REVERT: B 663 LEU cc_start: 0.8136 (mt) cc_final: 0.7862 (mt) REVERT: B 677 THR cc_start: 0.7163 (m) cc_final: 0.6799 (p) REVERT: B 682 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6206 (tp30) outliers start: 29 outliers final: 18 residues processed: 225 average time/residue: 0.2000 time to fit residues: 62.4369 Evaluate side-chains 216 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 58 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 0.0030 chunk 70 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9098 Z= 0.202 Angle : 0.664 10.559 12278 Z= 0.329 Chirality : 0.041 0.145 1370 Planarity : 0.004 0.066 1500 Dihedral : 12.025 62.174 1452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.12 % Allowed : 14.62 % 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: -1.26 (0.25), residues: 1046 helix: -0.30 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -1.90 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.008 0.002 HIS B 27 PHE 0.026 0.001 PHE A 65 TYR 0.021 0.002 TYR B 216 ARG 0.001 0.000 ARG A 69 *********************** 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 233 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 0.956 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 27 HIS cc_start: 0.6923 (t70) cc_final: 0.6671 (t70) REVERT: A 33 LYS cc_start: 0.8693 (pptt) cc_final: 0.8378 (ptpp) REVERT: A 115 LEU cc_start: 0.8022 (mt) cc_final: 0.7637 (mt) REVERT: A 119 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6806 (tm-30) REVERT: A 137 PHE cc_start: 0.8782 (t80) cc_final: 0.8249 (t80) REVERT: A 166 ASP cc_start: 0.8142 (t0) cc_final: 0.7614 (t0) REVERT: A 200 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7575 (ttp-170) REVERT: A 210 SER cc_start: 0.7979 (m) cc_final: 0.7548 (p) REVERT: A 290 LEU cc_start: 0.8844 (tp) cc_final: 0.8390 (mt) REVERT: A 319 MET cc_start: 0.7886 (tpt) cc_final: 0.7469 (tpt) REVERT: A 388 PHE cc_start: 0.7914 (t80) cc_final: 0.7535 (t80) REVERT: A 637 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6290 (tm-30) REVERT: A 682 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6310 (tp30) REVERT: B 96 ASN cc_start: 0.7880 (p0) cc_final: 0.7570 (p0) REVERT: B 115 LEU cc_start: 0.7874 (mt) cc_final: 0.7611 (mt) REVERT: B 137 PHE cc_start: 0.8784 (t80) cc_final: 0.8247 (t80) REVERT: B 166 ASP cc_start: 0.8128 (t0) cc_final: 0.7674 (t0) REVERT: B 210 SER cc_start: 0.8086 (m) cc_final: 0.7711 (p) REVERT: B 290 LEU cc_start: 0.8787 (tp) cc_final: 0.8394 (mt) REVERT: B 319 MET cc_start: 0.7867 (tpt) cc_final: 0.7459 (tpt) REVERT: B 324 ARG cc_start: 0.4985 (tpt-90) cc_final: 0.4683 (mtp180) REVERT: B 338 LYS cc_start: 0.8647 (mttt) cc_final: 0.7528 (tptp) REVERT: B 607 ASP cc_start: 0.7568 (t0) cc_final: 0.7290 (m-30) REVERT: B 682 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6138 (tp30) outliers start: 28 outliers final: 16 residues processed: 217 average time/residue: 0.2067 time to fit residues: 61.8826 Evaluate side-chains 209 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 347 CYS Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 650 THR 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 92 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3932 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= 0.211 Angle : 0.673 11.561 12278 Z= 0.332 Chirality : 0.042 0.146 1370 Planarity : 0.004 0.065 1500 Dihedral : 11.738 63.264 1452 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.35 % Allowed : 15.29 % Favored : 81.36 % 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: -0.84 (0.26), residues: 1046 helix: -0.01 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.018 0.001 PHE B 554 TYR 0.024 0.002 TYR B 107 ARG 0.002 0.000 ARG A 279 *********************** 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 231 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 0.901 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 27 HIS cc_start: 0.6891 (t70) cc_final: 0.6621 (t70) REVERT: A 115 LEU cc_start: 0.8039 (mt) cc_final: 0.7630 (mt) REVERT: A 119 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6759 (tm-30) REVERT: A 137 PHE cc_start: 0.8786 (t80) cc_final: 0.8267 (t80) REVERT: A 151 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6198 (ptm160) REVERT: A 166 ASP cc_start: 0.8198 (t0) cc_final: 0.7628 (t0) REVERT: A 200 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7628 (ttp-170) REVERT: A 210 SER cc_start: 0.8051 (m) cc_final: 0.7635 (p) REVERT: A 290 LEU cc_start: 0.8852 (tp) cc_final: 0.8393 (mp) REVERT: A 319 MET cc_start: 0.7899 (tpt) cc_final: 0.7500 (tpt) REVERT: A 663 LEU cc_start: 0.8495 (mm) cc_final: 0.8256 (mt) REVERT: A 673 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 96 ASN cc_start: 0.7865 (p0) cc_final: 0.7605 (p0) REVERT: B 115 LEU cc_start: 0.7885 (mt) cc_final: 0.7618 (mt) REVERT: B 137 PHE cc_start: 0.8778 (t80) cc_final: 0.8261 (t80) REVERT: B 166 ASP cc_start: 0.8285 (t0) cc_final: 0.7705 (t0) REVERT: B 210 SER cc_start: 0.8160 (m) cc_final: 0.7742 (p) REVERT: B 290 LEU cc_start: 0.8789 (tp) cc_final: 0.8346 (mt) REVERT: B 306 ASP cc_start: 0.8482 (t0) cc_final: 0.8028 (t0) REVERT: B 319 MET cc_start: 0.7824 (tpt) cc_final: 0.7451 (tpt) REVERT: B 324 ARG cc_start: 0.5009 (tpt-90) cc_final: 0.4698 (mtp180) REVERT: B 338 LYS cc_start: 0.8612 (mttt) cc_final: 0.7530 (tptp) REVERT: B 607 ASP cc_start: 0.7612 (t0) cc_final: 0.7322 (m-30) REVERT: B 663 LEU cc_start: 0.8700 (mm) cc_final: 0.8496 (mp) REVERT: B 682 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6129 (tp30) outliers start: 30 outliers final: 24 residues processed: 219 average time/residue: 0.2049 time to fit residues: 62.6645 Evaluate side-chains 216 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain 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 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE 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 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4003 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= 0.259 Angle : 0.694 10.641 12278 Z= 0.343 Chirality : 0.042 0.145 1370 Planarity : 0.005 0.067 1500 Dihedral : 11.840 62.773 1452 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.12 % Allowed : 16.29 % Favored : 80.58 % 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: -0.68 (0.26), residues: 1046 helix: 0.16 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.66 (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 0.018 0.001 PHE B 554 TYR 0.019 0.002 TYR B 256 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 226 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 0.997 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: A 27 HIS cc_start: 0.6920 (t70) cc_final: 0.6644 (t70) REVERT: A 33 LYS cc_start: 0.8780 (pptt) cc_final: 0.8289 (ptpp) REVERT: A 115 LEU cc_start: 0.8001 (mt) cc_final: 0.7564 (mt) REVERT: A 119 GLU cc_start: 0.7741 (mm-30) cc_final: 0.6761 (tm-30) REVERT: A 137 PHE cc_start: 0.8812 (t80) cc_final: 0.8283 (t80) REVERT: A 153 ASN cc_start: 0.8133 (m110) cc_final: 0.7919 (m110) REVERT: A 166 ASP cc_start: 0.8308 (t0) cc_final: 0.7694 (t0) REVERT: A 200 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7667 (ttp-170) REVERT: A 210 SER cc_start: 0.8093 (m) cc_final: 0.7679 (p) REVERT: A 290 LEU cc_start: 0.8804 (tp) cc_final: 0.8328 (mp) REVERT: A 319 MET cc_start: 0.7821 (tpt) cc_final: 0.7478 (tpt) REVERT: A 663 LEU cc_start: 0.8533 (mm) cc_final: 0.8270 (mt) REVERT: A 673 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 96 ASN cc_start: 0.7925 (p0) cc_final: 0.7683 (p0) REVERT: B 115 LEU cc_start: 0.7907 (mt) cc_final: 0.7627 (mt) REVERT: B 137 PHE cc_start: 0.8776 (t80) cc_final: 0.8242 (t80) REVERT: B 166 ASP cc_start: 0.8272 (t0) cc_final: 0.7722 (t0) REVERT: B 210 SER cc_start: 0.8096 (m) cc_final: 0.7674 (p) REVERT: B 306 ASP cc_start: 0.8412 (t0) cc_final: 0.8116 (t0) REVERT: B 319 MET cc_start: 0.7853 (tpt) cc_final: 0.7411 (tpt) REVERT: B 324 ARG cc_start: 0.5029 (tpt-90) cc_final: 0.4670 (mtp180) REVERT: B 607 ASP cc_start: 0.7628 (t0) cc_final: 0.7340 (m-30) REVERT: B 682 GLU cc_start: 0.6483 (mm-30) cc_final: 0.5910 (tp30) outliers start: 28 outliers final: 21 residues processed: 214 average time/residue: 0.1954 time to fit residues: 58.3484 Evaluate side-chains 214 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 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 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9098 Z= 0.209 Angle : 0.688 15.853 12278 Z= 0.334 Chirality : 0.041 0.147 1370 Planarity : 0.005 0.067 1500 Dihedral : 11.369 63.632 1452 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.68 % Allowed : 16.96 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.26), residues: 1046 helix: 0.30 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.027 0.001 PHE A 554 TYR 0.020 0.002 TYR B 216 ARG 0.001 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.925 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 27 HIS cc_start: 0.6917 (t70) cc_final: 0.6643 (t70) REVERT: A 33 LYS cc_start: 0.8753 (pptt) cc_final: 0.8305 (ptpp) REVERT: A 115 LEU cc_start: 0.8027 (mt) cc_final: 0.7626 (mt) REVERT: A 119 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6750 (tm-30) REVERT: A 137 PHE cc_start: 0.8787 (t80) cc_final: 0.8242 (t80) REVERT: A 142 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 153 ASN cc_start: 0.8267 (m110) cc_final: 0.8041 (m110) REVERT: A 166 ASP cc_start: 0.8290 (t0) cc_final: 0.7732 (t0) REVERT: A 200 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7647 (ttp-170) REVERT: A 210 SER cc_start: 0.8049 (m) cc_final: 0.7640 (p) REVERT: A 224 MET cc_start: 0.7500 (mtm) cc_final: 0.7201 (mtm) REVERT: A 290 LEU cc_start: 0.8823 (tp) cc_final: 0.8234 (mt) REVERT: A 319 MET cc_start: 0.7791 (tpt) cc_final: 0.7480 (tpt) REVERT: A 660 ILE cc_start: 0.4685 (OUTLIER) cc_final: 0.4293 (tp) REVERT: B 96 ASN cc_start: 0.7896 (p0) cc_final: 0.7689 (p0) REVERT: B 115 LEU cc_start: 0.7939 (mt) cc_final: 0.7692 (mt) REVERT: B 137 PHE cc_start: 0.8651 (t80) cc_final: 0.8118 (t80) REVERT: B 166 ASP cc_start: 0.8250 (t0) cc_final: 0.7736 (t0) REVERT: B 210 SER cc_start: 0.8070 (m) cc_final: 0.7689 (p) REVERT: B 262 PHE cc_start: 0.8602 (t80) cc_final: 0.8269 (t80) REVERT: B 290 LEU cc_start: 0.8819 (tp) cc_final: 0.8393 (mt) REVERT: B 306 ASP cc_start: 0.8379 (t0) cc_final: 0.8159 (t0) REVERT: B 319 MET cc_start: 0.7788 (tpt) cc_final: 0.7375 (tpt) REVERT: B 324 ARG cc_start: 0.4997 (tpt-90) cc_final: 0.4666 (mtp180) REVERT: B 682 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5959 (tp30) outliers start: 24 outliers final: 17 residues processed: 223 average time/residue: 0.1938 time to fit residues: 60.3775 Evaluate side-chains 215 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 206 LEU 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 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE 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 95 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4235 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= 0.248 Angle : 0.707 14.019 12278 Z= 0.343 Chirality : 0.042 0.147 1370 Planarity : 0.005 0.066 1500 Dihedral : 11.296 59.658 1450 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.46 % Allowed : 17.86 % Favored : 79.69 % 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: -0.45 (0.26), residues: 1046 helix: 0.34 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 92 HIS 0.007 0.002 HIS B 27 PHE 0.019 0.001 PHE B 554 TYR 0.023 0.002 TYR B 305 ARG 0.002 0.000 ARG B 552 *********************** 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 217 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 0.839 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: A 27 HIS cc_start: 0.6924 (t70) cc_final: 0.6639 (t70) REVERT: A 33 LYS cc_start: 0.8757 (pptt) cc_final: 0.8297 (ptpp) REVERT: A 119 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6863 (mm-30) REVERT: A 137 PHE cc_start: 0.8781 (t80) cc_final: 0.8229 (t80) REVERT: A 142 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8124 (mt-10) REVERT: A 153 ASN cc_start: 0.8297 (m110) cc_final: 0.8071 (m110) REVERT: A 166 ASP cc_start: 0.8356 (t0) cc_final: 0.7754 (t0) REVERT: A 200 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7651 (ttp-170) REVERT: A 210 SER cc_start: 0.7801 (m) cc_final: 0.7387 (p) REVERT: A 319 MET cc_start: 0.7798 (tpt) cc_final: 0.7487 (tpt) REVERT: A 346 GLN cc_start: 0.8320 (pt0) cc_final: 0.7808 (pm20) REVERT: A 676 PHE cc_start: 0.7220 (m-10) cc_final: 0.6944 (m-10) REVERT: B 96 ASN cc_start: 0.8021 (p0) cc_final: 0.7820 (p0) REVERT: B 137 PHE cc_start: 0.8705 (t80) cc_final: 0.8195 (t80) REVERT: B 166 ASP cc_start: 0.8242 (t0) cc_final: 0.7714 (t0) REVERT: B 210 SER cc_start: 0.7836 (m) cc_final: 0.7462 (p) REVERT: B 262 PHE cc_start: 0.8618 (t80) cc_final: 0.8382 (t80) REVERT: B 306 ASP cc_start: 0.8363 (t0) cc_final: 0.8159 (t0) REVERT: B 319 MET cc_start: 0.7800 (tpt) cc_final: 0.7384 (tpt) REVERT: B 324 ARG cc_start: 0.5080 (tpt-90) cc_final: 0.4697 (mtp180) REVERT: B 682 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6024 (tp30) outliers start: 22 outliers final: 18 residues processed: 210 average time/residue: 0.1906 time to fit residues: 55.5891 Evaluate side-chains 212 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 THR 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 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 658 ILE 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 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4374 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= 0.223 Angle : 0.695 13.875 12278 Z= 0.337 Chirality : 0.042 0.145 1370 Planarity : 0.005 0.065 1500 Dihedral : 11.004 59.849 1450 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.68 % Allowed : 17.52 % Favored : 79.80 % 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: -0.36 (0.26), residues: 1046 helix: 0.42 (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 0.022 0.001 TRP B 92 HIS 0.006 0.001 HIS B 27 PHE 0.022 0.001 PHE B 388 TYR 0.019 0.002 TYR B 305 ARG 0.002 0.000 ARG B 279 ********************** 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 227 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 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 27 HIS cc_start: 0.6930 (t70) cc_final: 0.6645 (t70) REVERT: A 119 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6823 (mm-30) REVERT: A 137 PHE cc_start: 0.8817 (t80) cc_final: 0.8290 (t80) REVERT: A 142 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 153 ASN cc_start: 0.8363 (m110) cc_final: 0.8146 (m110) REVERT: A 166 ASP cc_start: 0.8338 (t0) cc_final: 0.7760 (t0) REVERT: A 200 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7610 (ttp-170) REVERT: A 210 SER cc_start: 0.7773 (m) cc_final: 0.7376 (p) REVERT: A 224 MET cc_start: 0.7493 (mtm) cc_final: 0.7184 (mtm) REVERT: A 319 MET cc_start: 0.7774 (tpt) cc_final: 0.7473 (tpt) REVERT: A 346 GLN cc_start: 0.8278 (pt0) cc_final: 0.7831 (pm20) REVERT: B 137 PHE cc_start: 0.8706 (t80) cc_final: 0.8190 (t80) REVERT: B 166 ASP cc_start: 0.8223 (t0) cc_final: 0.7709 (t0) REVERT: B 210 SER cc_start: 0.7816 (m) cc_final: 0.7435 (p) REVERT: B 262 PHE cc_start: 0.8622 (t80) cc_final: 0.8391 (t80) REVERT: B 306 ASP cc_start: 0.8398 (t0) cc_final: 0.8163 (t0) REVERT: B 319 MET cc_start: 0.7779 (tpt) cc_final: 0.7367 (tpt) REVERT: B 324 ARG cc_start: 0.5086 (tpt-90) cc_final: 0.4702 (mtp180) REVERT: B 682 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6118 (tm-30) outliers start: 24 outliers final: 20 residues processed: 218 average time/residue: 0.1992 time to fit residues: 61.1265 Evaluate side-chains 213 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 215 THR 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 139 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.235398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184186 restraints weight = 9339.389| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.10 r_work: 0.3972 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9098 Z= 0.275 Angle : 0.725 13.569 12278 Z= 0.355 Chirality : 0.044 0.240 1370 Planarity : 0.005 0.066 1500 Dihedral : 11.290 59.215 1450 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.34 % Allowed : 18.19 % 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: -0.42 (0.26), residues: 1046 helix: 0.37 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 92 HIS 0.006 0.002 HIS B 27 PHE 0.019 0.001 PHE B 554 TYR 0.023 0.002 TYR B 305 ARG 0.005 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.57 seconds wall clock time: 41 minutes 3.17 seconds (2463.17 seconds total)