Starting phenix.real_space_refine on Wed Feb 14 08:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/02_2024/6e1m_8957_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/02_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_8957/02_2024/6e1m_8957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/02_2024/6e1m_8957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/02_2024/6e1m_8957_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1m_8957/02_2024/6e1m_8957_neut_updated.pdb" } 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 Residue "A ARG 62": "NH1" <-> "NH2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.30, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 3.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 0 sheets defined 63.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 36 through 43 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 52 through 55 No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 63 through 86 removed outlier: 3.656A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 118 through 135 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 138 through 141 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.622A pdb=" N TRP A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 154 through 172 removed outlier: 3.536A pdb=" N VAL A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.927A pdb=" N PHE A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 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 213 through 236 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 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 255 through 262 Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.134A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.521A pdb=" N SER A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 334 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 353 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 361 through 370 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 385 through 398 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 552 through 564 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 570 through 586 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 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 616 through 628 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 633 through 642 removed outlier: 3.918A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.855A pdb=" N TYR A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 683 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 685 through 691 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) Processing helix chain 'A' and resid 697 through 703 removed outlier: 3.544A pdb=" N ALA A 702 " --> pdb=" O ARG A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 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) Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 63 through 86 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) removed outlier: 3.542A pdb=" N SER B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASN B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 118 through 135 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 138 through 141 Processing helix chain 'B' and resid 155 through 172 removed outlier: 3.536A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.987A pdb=" N PHE B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.870A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 236 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 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 267 through 271 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 267 through 271' Processing helix chain 'B' and resid 279 through 294 removed outlier: 4.071A pdb=" N PHE B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 288 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 334 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 344 through 353 Processing helix chain 'B' and resid 361 through 370 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 385 through 398 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 552 through 564 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 570 through 586 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 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 602 through 605 No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 616 through 628 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 633 through 642 removed outlier: 3.871A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 662 removed outlier: 3.868A pdb=" N VAL B 653 " --> pdb=" O THR B 650 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 654 " --> pdb=" O TYR B 651 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 655 " --> pdb=" O PHE B 652 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 657 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 658 " --> pdb=" O PHE B 655 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 660 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 662 " --> pdb=" O THR B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 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 687 through 690 No H-bonds generated for 'chain 'B' and resid 687 through 690' Processing helix chain 'B' and resid 698 through 703 341 hydrogen bonds defined for protein. 948 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: 2.29 Time building geometry restraints manager: 3.86 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: 95.78 - 104.14: 132 104.14 - 112.50: 4390 112.50 - 120.86: 5275 120.86 - 129.21: 2409 129.21 - 137.57: 72 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: 83 2.56 - 3.15: 7112 3.15 - 3.73: 13406 3.73 - 4.32: 19653 4.32 - 4.90: 31285 Nonbonded interactions: 71539 Sorted by model distance: nonbonded pdb=" OH TYR B 114 " pdb=" OD2 ASP B 615 " model vdw 1.976 2.440 nonbonded pdb=" OH TYR A 114 " pdb=" OD2 ASP A 615 " model vdw 2.001 2.440 nonbonded pdb=" OH TYR A 305 " pdb=" OE2 GLU A 673 " model vdw 2.043 2.440 nonbonded pdb=" OH TYR B 305 " pdb=" OE2 GLU B 673 " model vdw 2.078 2.440 nonbonded pdb=" O TYR A 579 " pdb=" OH TYR A 651 " model vdw 2.151 2.440 ... (remaining 71534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.700 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: 4.080 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- 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= 1.118 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 : 0.875 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: 0.2182 time to fit residues: 85.2551 Evaluate side-chains 211 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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: 0.7139 moved from start: 0.2320 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= 0.241 Angle : 0.751 12.142 12278 Z= 0.381 Chirality : 0.042 0.185 1370 Planarity : 0.005 0.066 1500 Dihedral : 15.154 60.511 1452 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 1.79 % Allowed : 9.26 % Favored : 88.95 % 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: -3.81 (0.22), residues: 1046 helix: -2.45 (0.15), residues: 700 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 92 HIS 0.004 0.001 HIS B 27 PHE 0.017 0.002 PHE B 624 TYR 0.024 0.002 TYR B 63 ARG 0.009 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 244 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 0.975 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 33 LYS cc_start: 0.8685 (pptt) cc_final: 0.8353 (pptt) REVERT: A 115 LEU cc_start: 0.8150 (mt) cc_final: 0.7778 (mt) REVERT: A 119 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6882 (tm-30) REVERT: A 200 ARG cc_start: 0.8035 (ttp-110) cc_final: 0.7673 (ttp-170) REVERT: A 210 SER cc_start: 0.8561 (m) cc_final: 0.8054 (p) REVERT: A 279 ARG cc_start: 0.8956 (mmt-90) cc_final: 0.7766 (mtp85) REVERT: A 319 MET cc_start: 0.8094 (tpt) cc_final: 0.7524 (tpt) REVERT: A 605 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7757 (pt0) REVERT: A 607 ASP cc_start: 0.7967 (t70) cc_final: 0.7427 (m-30) REVERT: A 634 VAL cc_start: 0.8980 (t) cc_final: 0.8659 (m) REVERT: A 656 TYR cc_start: 0.8322 (t80) cc_final: 0.7773 (t80) REVERT: A 658 ILE cc_start: 0.8169 (mt) cc_final: 0.7934 (mm) REVERT: A 660 ILE cc_start: 0.5522 (mm) cc_final: 0.5310 (tp) REVERT: A 673 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 677 THR cc_start: 0.6855 (m) cc_final: 0.6453 (p) REVERT: A 678 GLU cc_start: 0.6716 (mp0) cc_final: 0.6214 (mp0) REVERT: A 682 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6337 (tp30) REVERT: B 115 LEU cc_start: 0.8002 (mt) cc_final: 0.7652 (mt) REVERT: B 200 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7509 (ttp-170) REVERT: B 210 SER cc_start: 0.8449 (m) cc_final: 0.8050 (p) REVERT: B 319 MET cc_start: 0.8030 (tpt) cc_final: 0.7563 (tpt) REVERT: B 324 ARG cc_start: 0.5334 (tpt-90) cc_final: 0.5096 (mmm160) REVERT: B 338 LYS cc_start: 0.8803 (mttt) cc_final: 0.7641 (tptt) REVERT: B 385 LYS cc_start: 0.7257 (ttmt) cc_final: 0.6835 (pttt) REVERT: B 607 ASP cc_start: 0.8115 (t0) cc_final: 0.7768 (t0) REVERT: B 634 VAL cc_start: 0.8616 (t) cc_final: 0.8268 (m) outliers start: 16 outliers final: 9 residues processed: 239 average time/residue: 0.2102 time to fit residues: 68.7278 Evaluate side-chains 219 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 347 CYS Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 638 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 0.0170 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 257 GLN B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2922 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= 0.181 Angle : 0.650 8.297 12278 Z= 0.327 Chirality : 0.040 0.139 1370 Planarity : 0.004 0.065 1500 Dihedral : 13.427 62.605 1452 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.12 % Allowed : 10.60 % Favored : 87.28 % 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: -2.77 (0.24), residues: 1046 helix: -1.57 (0.17), residues: 702 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 92 HIS 0.004 0.001 HIS B 27 PHE 0.017 0.001 PHE A 65 TYR 0.019 0.002 TYR B 141 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 248 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 1.042 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: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7913 (p0) cc_final: 0.7496 (p0) REVERT: A 115 LEU cc_start: 0.8134 (mt) cc_final: 0.7755 (mt) REVERT: A 119 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6851 (tm-30) REVERT: A 166 ASP cc_start: 0.8116 (t0) cc_final: 0.7561 (t0) REVERT: A 210 SER cc_start: 0.8507 (m) cc_final: 0.8004 (p) REVERT: A 279 ARG cc_start: 0.8844 (mmt-90) cc_final: 0.6240 (mmt180) REVERT: A 319 MET cc_start: 0.7932 (tpt) cc_final: 0.7517 (tpt) REVERT: A 388 PHE cc_start: 0.7724 (t80) cc_final: 0.7256 (t80) REVERT: A 607 ASP cc_start: 0.7782 (t70) cc_final: 0.7539 (m-30) REVERT: A 656 TYR cc_start: 0.8331 (t80) cc_final: 0.7952 (t80) REVERT: A 663 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 677 THR cc_start: 0.6835 (m) cc_final: 0.6468 (p) REVERT: A 682 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6302 (tp30) REVERT: B 43 ASP cc_start: 0.8647 (m-30) cc_final: 0.8404 (m-30) REVERT: B 115 LEU cc_start: 0.7889 (mt) cc_final: 0.7605 (mt) REVERT: B 210 SER cc_start: 0.8379 (m) cc_final: 0.7951 (p) REVERT: B 319 MET cc_start: 0.7946 (tpt) cc_final: 0.7494 (tpt) REVERT: B 324 ARG cc_start: 0.5091 (tpt-90) cc_final: 0.4382 (mtp180) REVERT: B 338 LYS cc_start: 0.8758 (mttt) cc_final: 0.7639 (tptt) REVERT: B 385 LYS cc_start: 0.7001 (ttmt) cc_final: 0.6778 (pttt) REVERT: B 607 ASP cc_start: 0.8034 (t0) cc_final: 0.7337 (m-30) REVERT: B 677 THR cc_start: 0.7027 (m) cc_final: 0.6667 (p) REVERT: B 682 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6007 (tp30) outliers start: 19 outliers final: 16 residues processed: 241 average time/residue: 0.2062 time to fit residues: 68.2571 Evaluate side-chains 226 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 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 A residue 650 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9098 Z= 0.244 Angle : 0.669 11.051 12278 Z= 0.330 Chirality : 0.042 0.153 1370 Planarity : 0.004 0.060 1500 Dihedral : 12.930 59.461 1452 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.79 % Allowed : 12.61 % Favored : 83.59 % 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: -2.09 (0.25), residues: 1046 helix: -1.04 (0.18), residues: 702 sheet: None (None), residues: 0 loop : -1.85 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 92 HIS 0.005 0.001 HIS B 27 PHE 0.025 0.002 PHE A 65 TYR 0.017 0.002 TYR A 141 ARG 0.003 0.000 ARG A 200 *********************** 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 254 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 0.967 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8635 (pptt) cc_final: 0.8322 (ptpp) REVERT: A 119 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 166 ASP cc_start: 0.7999 (t0) cc_final: 0.7541 (t0) REVERT: A 210 SER cc_start: 0.8535 (m) cc_final: 0.8042 (p) REVERT: A 319 MET cc_start: 0.7909 (tpt) cc_final: 0.7446 (tpt) REVERT: A 388 PHE cc_start: 0.7871 (t80) cc_final: 0.7511 (t80) REVERT: A 637 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6256 (tm-30) REVERT: A 660 ILE cc_start: 0.4867 (OUTLIER) cc_final: 0.4589 (tp) REVERT: A 663 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8005 (mt) REVERT: A 677 THR cc_start: 0.7003 (m) cc_final: 0.6569 (p) REVERT: A 682 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6276 (tp30) REVERT: B 96 ASN cc_start: 0.7964 (p0) cc_final: 0.7677 (p0) REVERT: B 115 LEU cc_start: 0.7907 (mt) cc_final: 0.7651 (mt) REVERT: B 142 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 166 ASP cc_start: 0.7962 (t0) cc_final: 0.7554 (t0) REVERT: B 210 SER cc_start: 0.8188 (m) cc_final: 0.7789 (p) REVERT: B 319 MET cc_start: 0.7899 (tpt) cc_final: 0.7466 (tpt) REVERT: B 324 ARG cc_start: 0.5075 (tpt-90) cc_final: 0.4738 (mtp180) REVERT: B 338 LYS cc_start: 0.8688 (mttt) cc_final: 0.7609 (tptt) REVERT: B 385 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6822 (pttt) REVERT: B 387 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8414 (mp0) REVERT: B 607 ASP cc_start: 0.7821 (t0) cc_final: 0.7340 (m-30) REVERT: B 663 LEU cc_start: 0.8215 (mt) cc_final: 0.7983 (mt) REVERT: B 677 THR cc_start: 0.7124 (m) cc_final: 0.6719 (p) REVERT: B 682 GLU cc_start: 0.6561 (mm-30) cc_final: 0.5990 (tp30) outliers start: 34 outliers final: 22 residues processed: 237 average time/residue: 0.2133 time to fit residues: 69.7908 Evaluate side-chains 233 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 658 ILE 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: 5.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9098 Z= 0.265 Angle : 0.664 8.987 12278 Z= 0.329 Chirality : 0.042 0.134 1370 Planarity : 0.004 0.059 1500 Dihedral : 12.740 59.968 1452 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.13 % Allowed : 14.17 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (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: -1.66 (0.25), residues: 1046 helix: -0.73 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.008 0.002 HIS A 27 PHE 0.019 0.002 PHE A 331 TYR 0.016 0.002 TYR B 256 ARG 0.011 0.000 ARG A 62 *********************** 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 257 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 0.926 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 33 LYS cc_start: 0.8610 (pptt) cc_final: 0.8314 (ptpp) REVERT: A 95 LYS cc_start: 0.7863 (tppt) cc_final: 0.7618 (ttpt) REVERT: A 119 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 166 ASP cc_start: 0.8147 (t0) cc_final: 0.7623 (t0) REVERT: A 210 SER cc_start: 0.8003 (m) cc_final: 0.7596 (p) REVERT: A 319 MET cc_start: 0.7940 (tpt) cc_final: 0.7510 (tpt) REVERT: A 388 PHE cc_start: 0.7865 (t80) cc_final: 0.7568 (t80) REVERT: A 637 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6302 (tm-30) REVERT: A 660 ILE cc_start: 0.5074 (OUTLIER) cc_final: 0.4727 (tp) REVERT: A 663 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8023 (mt) REVERT: A 677 THR cc_start: 0.7113 (m) cc_final: 0.6632 (p) REVERT: A 682 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6352 (tp30) REVERT: B 95 LYS cc_start: 0.7805 (tppt) cc_final: 0.7493 (ttpt) REVERT: B 96 ASN cc_start: 0.7969 (p0) cc_final: 0.7662 (p0) REVERT: B 115 LEU cc_start: 0.7926 (mt) cc_final: 0.7657 (mt) REVERT: B 166 ASP cc_start: 0.7971 (t0) cc_final: 0.7551 (t0) REVERT: B 210 SER cc_start: 0.7996 (m) cc_final: 0.7623 (p) REVERT: B 319 MET cc_start: 0.7960 (tpt) cc_final: 0.7517 (tpt) REVERT: B 324 ARG cc_start: 0.5015 (tpt-90) cc_final: 0.4686 (mtp180) REVERT: B 338 LYS cc_start: 0.8681 (mttt) cc_final: 0.7609 (tptt) REVERT: B 387 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7630 (mp0) REVERT: B 607 ASP cc_start: 0.7802 (t0) cc_final: 0.7332 (m-30) REVERT: B 637 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6423 (tm-30) REVERT: B 663 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 677 THR cc_start: 0.7110 (m) cc_final: 0.6693 (p) REVERT: B 682 GLU cc_start: 0.6496 (mm-30) cc_final: 0.5919 (tp30) outliers start: 37 outliers final: 28 residues processed: 238 average time/residue: 0.2035 time to fit residues: 67.1671 Evaluate side-chains 243 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9098 Z= 0.215 Angle : 0.629 9.125 12278 Z= 0.311 Chirality : 0.041 0.178 1370 Planarity : 0.004 0.064 1500 Dihedral : 12.167 59.938 1452 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.46 % Allowed : 15.07 % Favored : 80.47 % 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: -1.34 (0.26), residues: 1046 helix: -0.47 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 92 HIS 0.006 0.002 HIS A 27 PHE 0.019 0.001 PHE B 554 TYR 0.023 0.002 TYR B 107 ARG 0.004 0.000 ARG A 200 *********************** 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 257 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8620 (pptt) cc_final: 0.8352 (ptpp) REVERT: A 95 LYS cc_start: 0.7864 (tppt) cc_final: 0.7658 (ttpt) REVERT: A 119 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 137 PHE cc_start: 0.8692 (t80) cc_final: 0.8226 (t80) REVERT: A 166 ASP cc_start: 0.8161 (t0) cc_final: 0.7640 (t0) REVERT: A 210 SER cc_start: 0.8000 (m) cc_final: 0.7577 (p) REVERT: A 319 MET cc_start: 0.7853 (tpt) cc_final: 0.7461 (tpt) REVERT: A 388 PHE cc_start: 0.7902 (t80) cc_final: 0.7564 (t80) REVERT: A 637 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6299 (tm-30) REVERT: A 660 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4507 (tp) REVERT: A 663 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7929 (mt) REVERT: A 677 THR cc_start: 0.6942 (m) cc_final: 0.6504 (p) REVERT: A 682 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6443 (tp30) REVERT: B 96 ASN cc_start: 0.7917 (p0) cc_final: 0.7613 (p0) REVERT: B 115 LEU cc_start: 0.7898 (mt) cc_final: 0.7697 (mt) REVERT: B 137 PHE cc_start: 0.8653 (t80) cc_final: 0.8137 (t80) REVERT: B 142 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 166 ASP cc_start: 0.8208 (t0) cc_final: 0.7633 (t0) REVERT: B 210 SER cc_start: 0.8082 (m) cc_final: 0.7662 (p) REVERT: B 319 MET cc_start: 0.7918 (tpt) cc_final: 0.7502 (tpt) REVERT: B 324 ARG cc_start: 0.4957 (tpt-90) cc_final: 0.4639 (mtp180) REVERT: B 338 LYS cc_start: 0.8657 (mttt) cc_final: 0.7575 (tptt) REVERT: B 566 MET cc_start: 0.8685 (mmm) cc_final: 0.8351 (mmm) REVERT: B 607 ASP cc_start: 0.7727 (t0) cc_final: 0.7358 (m-30) REVERT: B 637 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6435 (tm-30) REVERT: B 656 TYR cc_start: 0.8457 (t80) cc_final: 0.7587 (t80) REVERT: B 677 THR cc_start: 0.6952 (m) cc_final: 0.6555 (p) REVERT: B 682 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5934 (tp30) outliers start: 40 outliers final: 26 residues processed: 235 average time/residue: 0.1964 time to fit residues: 64.0983 Evaluate side-chains 236 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3720 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= 0.231 Angle : 0.640 9.090 12278 Z= 0.314 Chirality : 0.042 0.175 1370 Planarity : 0.004 0.061 1500 Dihedral : 11.793 59.522 1450 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.79 % Allowed : 16.52 % Favored : 79.69 % 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: -1.10 (0.26), residues: 1046 helix: -0.29 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.51 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.006 0.002 HIS A 27 PHE 0.019 0.001 PHE A 331 TYR 0.016 0.002 TYR B 251 ARG 0.007 0.000 ARG A 200 *********************** 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 245 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 0.888 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 33 LYS cc_start: 0.8617 (pptt) cc_final: 0.8351 (ptpp) REVERT: A 96 ASN cc_start: 0.8045 (p0) cc_final: 0.7756 (p0) REVERT: A 137 PHE cc_start: 0.8698 (t80) cc_final: 0.8234 (t80) REVERT: A 153 ASN cc_start: 0.8207 (m110) cc_final: 0.7942 (m110) REVERT: A 166 ASP cc_start: 0.8250 (t0) cc_final: 0.7631 (t0) REVERT: A 210 SER cc_start: 0.8272 (m) cc_final: 0.7901 (p) REVERT: A 213 LEU cc_start: 0.9022 (mm) cc_final: 0.8789 (mm) REVERT: A 319 MET cc_start: 0.7802 (tpt) cc_final: 0.7431 (tpt) REVERT: A 388 PHE cc_start: 0.7919 (t80) cc_final: 0.7527 (t80) REVERT: A 637 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6329 (tm-30) REVERT: A 660 ILE cc_start: 0.4621 (OUTLIER) cc_final: 0.4192 (tp) REVERT: A 677 THR cc_start: 0.6876 (m) cc_final: 0.6424 (p) REVERT: A 682 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6453 (tp30) REVERT: B 95 LYS cc_start: 0.7832 (tppt) cc_final: 0.7234 (ttpt) REVERT: B 96 ASN cc_start: 0.7900 (p0) cc_final: 0.7602 (p0) REVERT: B 137 PHE cc_start: 0.8658 (t80) cc_final: 0.8084 (t80) REVERT: B 166 ASP cc_start: 0.8208 (t0) cc_final: 0.7661 (t0) REVERT: B 210 SER cc_start: 0.7921 (m) cc_final: 0.7509 (p) REVERT: B 213 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8549 (mm) REVERT: B 319 MET cc_start: 0.7853 (tpt) cc_final: 0.7401 (tpt) REVERT: B 324 ARG cc_start: 0.4977 (tpt-90) cc_final: 0.4592 (mtp180) REVERT: B 387 GLU cc_start: 0.8436 (mp0) cc_final: 0.7693 (mp0) REVERT: B 566 MET cc_start: 0.8625 (mmm) cc_final: 0.8320 (mmm) REVERT: B 605 GLU cc_start: 0.7798 (pt0) cc_final: 0.7525 (pt0) REVERT: B 607 ASP cc_start: 0.7693 (t0) cc_final: 0.7341 (m-30) REVERT: B 637 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 656 TYR cc_start: 0.8474 (t80) cc_final: 0.7658 (t80) REVERT: B 677 THR cc_start: 0.6982 (m) cc_final: 0.6608 (p) REVERT: B 682 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5909 (tp30) outliers start: 34 outliers final: 24 residues processed: 229 average time/residue: 0.2010 time to fit residues: 64.1659 Evaluate side-chains 231 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9098 Z= 0.213 Angle : 0.624 9.382 12278 Z= 0.307 Chirality : 0.041 0.198 1370 Planarity : 0.004 0.066 1500 Dihedral : 11.392 59.856 1450 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.68 % Allowed : 17.41 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1046 helix: -0.02 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.006 0.002 HIS A 27 PHE 0.019 0.001 PHE B 554 TYR 0.020 0.002 TYR B 107 ARG 0.008 0.000 ARG A 200 *********************** 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 246 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 1.012 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8587 (pptt) cc_final: 0.8350 (ptpp) REVERT: A 111 GLU cc_start: 0.6871 (tp30) cc_final: 0.6168 (tp30) REVERT: A 137 PHE cc_start: 0.8730 (t80) cc_final: 0.8151 (t80) REVERT: A 153 ASN cc_start: 0.8266 (m110) cc_final: 0.8020 (m110) REVERT: A 166 ASP cc_start: 0.8232 (t0) cc_final: 0.7660 (t0) REVERT: A 210 SER cc_start: 0.8187 (m) cc_final: 0.7909 (p) REVERT: A 213 LEU cc_start: 0.8852 (mm) cc_final: 0.8533 (mm) REVERT: A 224 MET cc_start: 0.7522 (mtm) cc_final: 0.7205 (mtm) REVERT: A 319 MET cc_start: 0.7818 (tpt) cc_final: 0.7499 (tpt) REVERT: A 388 PHE cc_start: 0.7953 (t80) cc_final: 0.7560 (t80) REVERT: A 637 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6344 (tm-30) REVERT: A 660 ILE cc_start: 0.4498 (OUTLIER) cc_final: 0.4063 (tp) REVERT: A 677 THR cc_start: 0.6971 (m) cc_final: 0.6537 (p) REVERT: A 682 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6435 (tp30) REVERT: B 96 ASN cc_start: 0.8003 (p0) cc_final: 0.7704 (p0) REVERT: B 137 PHE cc_start: 0.8682 (t80) cc_final: 0.8110 (t80) REVERT: B 142 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 166 ASP cc_start: 0.8191 (t0) cc_final: 0.7663 (t0) REVERT: B 210 SER cc_start: 0.8093 (m) cc_final: 0.7619 (p) REVERT: B 213 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 319 MET cc_start: 0.7829 (tpt) cc_final: 0.7384 (tpt) REVERT: B 324 ARG cc_start: 0.4969 (tpt-90) cc_final: 0.4578 (mtp180) REVERT: B 566 MET cc_start: 0.8657 (mmm) cc_final: 0.8349 (mmm) REVERT: B 605 GLU cc_start: 0.7735 (pt0) cc_final: 0.7456 (pt0) REVERT: B 607 ASP cc_start: 0.7595 (t0) cc_final: 0.7310 (m-30) REVERT: B 637 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 656 TYR cc_start: 0.8484 (t80) cc_final: 0.7647 (t80) REVERT: B 677 THR cc_start: 0.6962 (m) cc_final: 0.6595 (p) REVERT: B 682 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5960 (tp30) outliers start: 33 outliers final: 22 residues processed: 233 average time/residue: 0.2024 time to fit residues: 65.6338 Evaluate side-chains 229 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9098 Z= 0.208 Angle : 0.631 12.846 12278 Z= 0.307 Chirality : 0.041 0.173 1370 Planarity : 0.004 0.064 1500 Dihedral : 11.062 59.940 1450 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.01 % Allowed : 18.75 % Favored : 78.24 % 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: -0.71 (0.26), residues: 1046 helix: 0.15 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.006 0.002 HIS A 27 PHE 0.019 0.001 PHE B 388 TYR 0.021 0.002 TYR A 107 ARG 0.007 0.000 ARG A 200 *********************** 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 236 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.016 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8608 (pptt) cc_final: 0.8392 (ptpp) REVERT: A 111 GLU cc_start: 0.6945 (tp30) cc_final: 0.6204 (tp30) REVERT: A 137 PHE cc_start: 0.8723 (t80) cc_final: 0.8149 (t80) REVERT: A 142 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 153 ASN cc_start: 0.8296 (m110) cc_final: 0.8067 (m110) REVERT: A 166 ASP cc_start: 0.8221 (t0) cc_final: 0.7664 (t0) REVERT: A 210 SER cc_start: 0.8196 (m) cc_final: 0.7885 (p) REVERT: A 213 LEU cc_start: 0.8765 (mm) cc_final: 0.8442 (mm) REVERT: A 224 MET cc_start: 0.7513 (mtm) cc_final: 0.7184 (mtm) REVERT: A 319 MET cc_start: 0.7798 (tpt) cc_final: 0.7484 (tpt) REVERT: A 585 GLN cc_start: 0.7222 (mt0) cc_final: 0.6908 (mt0) REVERT: A 637 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6342 (tm-30) REVERT: A 660 ILE cc_start: 0.4261 (OUTLIER) cc_final: 0.3818 (tp) REVERT: A 677 THR cc_start: 0.6916 (m) cc_final: 0.6473 (p) REVERT: B 95 LYS cc_start: 0.7679 (tppt) cc_final: 0.7211 (ttpt) REVERT: B 96 ASN cc_start: 0.7975 (p0) cc_final: 0.7701 (p0) REVERT: B 137 PHE cc_start: 0.8724 (t80) cc_final: 0.8173 (t80) REVERT: B 166 ASP cc_start: 0.8181 (t0) cc_final: 0.7660 (t0) REVERT: B 210 SER cc_start: 0.8032 (m) cc_final: 0.7527 (p) REVERT: B 213 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8351 (mm) REVERT: B 319 MET cc_start: 0.7809 (tpt) cc_final: 0.7377 (tpt) REVERT: B 324 ARG cc_start: 0.4965 (tpt-90) cc_final: 0.4570 (mtp180) REVERT: B 566 MET cc_start: 0.8651 (mmm) cc_final: 0.8346 (mmm) REVERT: B 605 GLU cc_start: 0.7700 (pt0) cc_final: 0.7444 (pt0) REVERT: B 607 ASP cc_start: 0.7545 (t0) cc_final: 0.7325 (m-30) REVERT: B 637 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6466 (tm-30) REVERT: B 656 TYR cc_start: 0.8485 (t80) cc_final: 0.8249 (t80) REVERT: B 677 THR cc_start: 0.6953 (m) cc_final: 0.6585 (p) REVERT: B 682 GLU cc_start: 0.6480 (mm-30) cc_final: 0.6141 (tm-30) outliers start: 27 outliers final: 22 residues processed: 226 average time/residue: 0.1986 time to fit residues: 62.3167 Evaluate side-chains 227 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9098 Z= 0.212 Angle : 0.634 11.897 12278 Z= 0.309 Chirality : 0.041 0.160 1370 Planarity : 0.004 0.063 1500 Dihedral : 10.882 59.806 1450 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.90 % Allowed : 19.31 % Favored : 77.79 % 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: -0.57 (0.27), residues: 1046 helix: 0.24 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.62 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.009 0.002 HIS A 27 PHE 0.019 0.001 PHE A 331 TYR 0.020 0.002 TYR B 107 ARG 0.009 0.000 ARG A 200 ********************** 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 228 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 0.991 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 111 GLU cc_start: 0.7041 (tp30) cc_final: 0.6265 (tp30) REVERT: A 137 PHE cc_start: 0.8747 (t80) cc_final: 0.8173 (t80) REVERT: A 142 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 166 ASP cc_start: 0.8232 (t0) cc_final: 0.7672 (t0) REVERT: A 210 SER cc_start: 0.7844 (m) cc_final: 0.7513 (p) REVERT: A 213 LEU cc_start: 0.8746 (mm) cc_final: 0.8426 (mm) REVERT: A 224 MET cc_start: 0.7504 (mtm) cc_final: 0.7176 (mtm) REVERT: A 319 MET cc_start: 0.7783 (tpt) cc_final: 0.7480 (tpt) REVERT: A 637 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 677 THR cc_start: 0.6949 (m) cc_final: 0.6493 (p) REVERT: B 95 LYS cc_start: 0.7577 (tppt) cc_final: 0.7188 (ttpt) REVERT: B 96 ASN cc_start: 0.7979 (p0) cc_final: 0.7705 (p0) REVERT: B 137 PHE cc_start: 0.8737 (t80) cc_final: 0.8200 (t80) REVERT: B 166 ASP cc_start: 0.8175 (t0) cc_final: 0.7664 (t0) REVERT: B 210 SER cc_start: 0.8019 (m) cc_final: 0.7501 (p) REVERT: B 213 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8440 (mm) REVERT: B 319 MET cc_start: 0.7801 (tpt) cc_final: 0.7379 (tpt) REVERT: B 324 ARG cc_start: 0.5024 (tpt-90) cc_final: 0.4624 (mtp180) REVERT: B 387 GLU cc_start: 0.8465 (mp0) cc_final: 0.7718 (mp0) REVERT: B 566 MET cc_start: 0.8640 (mmm) cc_final: 0.8336 (mmm) REVERT: B 605 GLU cc_start: 0.7683 (pt0) cc_final: 0.7411 (pt0) REVERT: B 607 ASP cc_start: 0.7539 (t0) cc_final: 0.7267 (m-30) REVERT: B 626 LEU cc_start: 0.8422 (mp) cc_final: 0.8214 (mp) REVERT: B 637 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 656 TYR cc_start: 0.8616 (t80) cc_final: 0.8181 (t80) REVERT: B 677 THR cc_start: 0.6951 (m) cc_final: 0.6587 (p) REVERT: B 682 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6147 (tm-30) outliers start: 26 outliers final: 22 residues processed: 219 average time/residue: 0.1999 time to fit residues: 60.9233 Evaluate side-chains 226 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 659 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 194 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 chunk 4 optimal weight: 5.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.236093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.186484 restraints weight = 9298.078| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.94 r_work: 0.4010 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9098 Z= 0.181 Angle : 0.616 11.411 12278 Z= 0.300 Chirality : 0.040 0.155 1370 Planarity : 0.004 0.058 1500 Dihedral : 10.424 59.922 1450 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.46 % Allowed : 19.87 % Favored : 77.68 % 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: -0.37 (0.27), residues: 1046 helix: 0.41 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.008 0.002 HIS A 27 PHE 0.021 0.001 PHE B 388 TYR 0.019 0.002 TYR A 141 ARG 0.009 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.40 seconds wall clock time: 43 minutes 19.77 seconds (2599.77 seconds total)