Starting phenix.real_space_refine on Thu Feb 5 00:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.map" model { file = "/net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p1m_71128/02_2026/9p1m_71128.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 62 5.16 5 C 8813 2.51 5 N 2329 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3879 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3988 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 498} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1561 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1609 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 169} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1448 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 183} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.67, per 1000 atoms: 0.26 Number of scatterers: 13874 At special positions: 0 Unit cell: (83.8035, 147.291, 125.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 62 16.00 O 2666 8.00 N 2329 7.00 C 8813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 311 " " NAG B 601 " - " ASN B 311 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 462.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 220 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 38 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 220 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 243 " pdb="ZN ZN B 602 " - pdb="ZN ZN B 603 " 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 22.8% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 53 through 57 removed outlier: 4.077A pdb=" N CYS A 57 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 148 through 155 removed outlier: 4.102A pdb=" N SER A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 195 through 210 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.638A pdb=" N ILE A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.589A pdb=" N VAL A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.798A pdb=" N LYS A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 513' Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.541A pdb=" N CYS B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.635A pdb=" N THR B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.630A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.982A pdb=" N GLN B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 195 through 210 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.731A pdb=" N ILE B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.589A pdb=" N VAL B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 508 through 514 removed outlier: 3.760A pdb=" N LYS B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.622A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.651A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.752A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.522A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 removed outlier: 6.564A pdb=" N MET A 113 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 112 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A 79 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR A 30 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 81 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 32 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 407 removed outlier: 7.086A pdb=" N ILE A 406 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE A 538 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS A 341 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 453 removed outlier: 7.247A pdb=" N MET A 386 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ILE A 388 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 486 Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.524A pdb=" N MET B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA B 112 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 80 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA B 114 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 82 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LEU B 79 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 30 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 81 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 32 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR B 289 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 305 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS B 291 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B 303 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 293 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.524A pdb=" N MET B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA B 112 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 80 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA B 114 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 82 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LEU B 79 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 30 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 81 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 32 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.781A pdb=" N VAL B 239 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.620A pdb=" N GLY B 340 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ILE B 538 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS B 341 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 450 through 453 removed outlier: 6.844A pdb=" N MET B 386 " --> pdb=" O ILE B 496 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE B 388 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 517 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 484 through 486 removed outlier: 7.738A pdb=" N LYS B 547 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 457 " --> pdb=" O LYS B 547 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.523A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.437A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.263A pdb=" N SER C 131 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 181 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL C 133 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 179 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU C 135 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N SER C 177 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN C 137 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 175 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.632A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.660A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.667A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 130 through 134 removed outlier: 5.266A pdb=" N ALA D 147 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 194 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLY D 149 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 192 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU D 151 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER D 190 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS D 153 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 188 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 130 through 134 removed outlier: 5.266A pdb=" N ALA D 147 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 194 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLY D 149 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 192 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU D 151 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER D 190 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS D 153 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 188 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 161 through 164 removed outlier: 4.145A pdb=" N TYR D 204 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.792A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA E 50 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.650A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.298A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.700A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 130 through 134 removed outlier: 4.334A pdb=" N ALA F 146 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 130 through 134 removed outlier: 4.334A pdb=" N ALA F 146 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 161 through 163 585 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2424 1.32 - 1.44: 3697 1.44 - 1.57: 7959 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 14172 Sorted by residual: bond pdb=" CA TYR A 87 " pdb=" C TYR A 87 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.22e-02 6.72e+03 2.11e+01 bond pdb=" CA ALA A 142 " pdb=" CB ALA A 142 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.74e-02 3.30e+03 1.53e+01 bond pdb=" CA GLY A 89 " pdb=" C GLY A 89 " ideal model delta sigma weight residual 1.514 1.463 0.052 1.41e-02 5.03e+03 1.35e+01 bond pdb=" C ILE A 139 " pdb=" O ILE A 139 " ideal model delta sigma weight residual 1.238 1.200 0.038 1.09e-02 8.42e+03 1.21e+01 bond pdb=" CA SER A 141 " pdb=" CB SER A 141 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.69e-02 3.50e+03 8.98e+00 ... (remaining 14167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 19060 2.76 - 5.52: 192 5.52 - 8.28: 28 8.28 - 11.04: 2 11.04 - 13.80: 2 Bond angle restraints: 19284 Sorted by residual: angle pdb=" C ALA A 142 " pdb=" N ASN A 143 " pdb=" CA ASN A 143 " ideal model delta sigma weight residual 122.37 110.62 11.75 1.54e+00 4.22e-01 5.83e+01 angle pdb=" C GLY A 89 " pdb=" N THR A 90 " pdb=" CA THR A 90 " ideal model delta sigma weight residual 121.54 107.74 13.80 1.91e+00 2.74e-01 5.22e+01 angle pdb=" N PRO D 223 " pdb=" CA PRO D 223 " pdb=" CB PRO D 223 " ideal model delta sigma weight residual 103.33 110.15 -6.82 1.10e+00 8.26e-01 3.84e+01 angle pdb=" CA TYR A 87 " pdb=" CB TYR A 87 " pdb=" CG TYR A 87 " ideal model delta sigma weight residual 113.90 124.36 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 113.23 106.27 6.96 1.24e+00 6.50e-01 3.15e+01 ... (remaining 19279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7641 17.87 - 35.74: 591 35.74 - 53.61: 164 53.61 - 71.49: 27 71.49 - 89.36: 12 Dihedral angle restraints: 8435 sinusoidal: 3161 harmonic: 5274 Sorted by residual: dihedral pdb=" CD ARG C 24 " pdb=" NE ARG C 24 " pdb=" CZ ARG C 24 " pdb=" NH1 ARG C 24 " ideal model delta sinusoidal sigma weight residual 0.00 80.53 -80.53 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CD ARG A 328 " pdb=" NE ARG A 328 " pdb=" CZ ARG A 328 " pdb=" NH1 ARG A 328 " ideal model delta sinusoidal sigma weight residual 0.00 -56.94 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS F 150 " pdb=" SG CYS F 150 " pdb=" SG CYS F 206 " pdb=" CB CYS F 206 " ideal model delta sinusoidal sigma weight residual 93.00 50.95 42.05 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 8432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1750 0.051 - 0.102: 344 0.102 - 0.153: 103 0.153 - 0.205: 7 0.205 - 0.256: 4 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CA GLN A 88 " pdb=" N GLN A 88 " pdb=" C GLN A 88 " pdb=" CB GLN A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA GLN C 155 " pdb=" N GLN C 155 " pdb=" C GLN C 155 " pdb=" CB GLN C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO D 223 " pdb=" N PRO D 223 " pdb=" C PRO D 223 " pdb=" CB PRO D 223 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2205 not shown) Planarity restraints: 2484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 24 " -1.080 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG C 24 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 24 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 24 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 24 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " -0.927 9.50e-02 1.11e+02 4.15e-01 1.05e+02 pdb=" NE ARG A 328 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 138 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C PRO A 138 " 0.078 2.00e-02 2.50e+03 pdb=" O PRO A 138 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE A 139 " -0.026 2.00e-02 2.50e+03 ... (remaining 2481 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 40 2.64 - 3.20: 12230 3.20 - 3.77: 22023 3.77 - 4.33: 32671 4.33 - 4.90: 52570 Nonbonded interactions: 119534 Sorted by model distance: nonbonded pdb=" OD1 ASN B 117 " pdb="ZN ZN B 602 " model vdw 2.070 2.230 nonbonded pdb=" OD2 ASP A 85 " pdb="ZN ZN A 603 " model vdw 2.131 2.230 nonbonded pdb=" ND2 ASN A 117 " pdb="ZN ZN A 602 " model vdw 2.153 2.310 nonbonded pdb=" OD2 ASP A 85 " pdb="ZN ZN A 602 " model vdw 2.174 2.230 nonbonded pdb=" OD2 ASP B 85 " pdb="ZN ZN B 602 " model vdw 2.220 2.230 ... (remaining 119529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 47 through 178 or (resid 179 and ( \ name N or name CA or name C or name O or name CB or name CG )) or resid 180 thro \ ugh 273 or (resid 274 and (name N or name CA or name C or name O or name CB or n \ ame CG )) or resid 275 through 439 or (resid 440 through 441 and (name N or name \ CA or name C or name O or name CB )) or resid 442 through 462 or (resid 463 thr \ ough 464 and (name N or name CA or name C or name O or name CB )) or resid 465 t \ hrough 466 or (resid 467 and (name N or name CA or name C or name O or name CB ) \ ) or resid 468 through 603)) selection = (chain 'B' and (resid 27 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 or (resid 52 and (name N or name CA or nam \ e C or name O or name CB )) or resid 53 through 54 or (resid 55 through 56 and ( \ name N or name CA or name C or name O or name CB )) or resid 57 through 135 or ( \ resid 136 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD )) or resid 137 through 151 or (resid 152 through 153 and (name N or name \ CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name N or n \ ame CA or name C or name O or name CB )) or resid 156 through 233 or (resid 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 25 \ 1 or (resid 252 and (name N or name CA or name C or name O or name CB )) or resi \ d 253 through 270 or (resid 271 and (name N or name CA or name C or name O or na \ me CB )) or resid 272 through 325 or (resid 326 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 327 through 336 or (resi \ d 337 and (name N or name CA or name C or name O or name CB )) or resid 338 thro \ ugh 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) o \ r resid 352 through 373 or (resid 374 and (name N or name CA or name C or name O \ or name CB )) or resid 381 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 408 or (resid 409 and (name \ N or name CA or name C or name O or name CB )) or resid 410 through 426 or (resi \ d 427 and (name N or name CA or name C or name O or name CB )) or resid 428 thro \ ugh 432 or (resid 433 through 434 and (name N or name CA or name C or name O or \ name CB )) or resid 435 through 470 or (resid 471 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 472 through 479 or (re \ sid 480 and (name N or name CA or name C or name O or name CB )) or resid 481 th \ rough 487 or (resid 488 through 491 and (name N or name CA or name C or name O o \ r name CB )) or resid 492 through 511 or (resid 512 and (name N or name CA or na \ me C or name O or name CB )) or resid 513 through 535 or (resid 536 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 537 \ through 603)) } ncs_group { reference = (chain 'C' and (resid 1 through 121 or resid 132 through 150 or (resid 155 and ( \ name N or name CA or name C or name O or name CB )) or resid 156 through 179 or \ resid 191 through 201 or resid 204 through 208)) selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 1 through 134 or resid 145 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 164 or \ resid 173 through 194 or resid 205 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221)) selection = (chain 'F' and (resid 1 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 221)) } 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.430 Find NCS groups from input model: 0.300 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.004 0.068 14193 Z= 0.204 Angle : 0.731 13.804 19318 Z= 0.429 Chirality : 0.047 0.256 2208 Planarity : 0.014 0.484 2482 Dihedral : 14.222 89.357 5021 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % Rotamer: Outliers : 0.20 % Allowed : 12.77 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1813 helix: 0.31 (0.29), residues: 331 sheet: 0.08 (0.21), residues: 569 loop : 0.12 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 87 TYR 0.017 0.001 TYR A 87 PHE 0.022 0.001 PHE A 421 TRP 0.012 0.001 TRP A 327 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00364 (14172) covalent geometry : angle 0.72799 (19284) SS BOND : bond 0.00151 ( 14) SS BOND : angle 0.96699 ( 28) hydrogen bonds : bond 0.11058 ( 547) hydrogen bonds : angle 7.00855 ( 1542) metal coordination : bond 0.00194 ( 5) link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 3.25347 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7865 (ttt-90) REVERT: A 403 ASN cc_start: 0.7895 (m110) cc_final: 0.7632 (m110) REVERT: A 446 THR cc_start: 0.7724 (OUTLIER) cc_final: 0.7485 (p) REVERT: C 207 LYS cc_start: 0.7798 (tppt) cc_final: 0.7295 (mmmt) REVERT: D 219 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7840 (tptp) REVERT: E 116 PHE cc_start: 0.7718 (m-80) cc_final: 0.7497 (m-80) outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.7187 time to fit residues: 123.0718 Evaluate side-chains 148 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 147 GLN D 207 ASN F 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065479 restraints weight = 32864.565| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.81 r_work: 0.3049 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14193 Z= 0.099 Angle : 0.514 5.604 19318 Z= 0.267 Chirality : 0.044 0.166 2208 Planarity : 0.004 0.047 2482 Dihedral : 5.015 58.384 2005 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 1.82 % Allowed : 12.16 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1813 helix: 0.60 (0.30), residues: 326 sheet: 0.18 (0.22), residues: 560 loop : 0.19 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 356 TYR 0.015 0.001 TYR C 49 PHE 0.013 0.001 PHE A 104 TRP 0.009 0.001 TRP F 47 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00217 (14172) covalent geometry : angle 0.51329 (19284) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.66177 ( 28) hydrogen bonds : bond 0.02943 ( 547) hydrogen bonds : angle 5.57434 ( 1542) metal coordination : bond 0.00184 ( 5) link_NAG-ASN : bond 0.00089 ( 2) link_NAG-ASN : angle 1.74410 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 403 ASN cc_start: 0.7815 (m110) cc_final: 0.7551 (m-40) REVERT: C 142 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.8172 (ttt-90) REVERT: C 207 LYS cc_start: 0.7766 (tppt) cc_final: 0.7140 (mmmt) REVERT: E 116 PHE cc_start: 0.7641 (m-80) cc_final: 0.7391 (m-80) REVERT: F 67 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8258 (mtm110) outliers start: 27 outliers final: 13 residues processed: 177 average time/residue: 0.6323 time to fit residues: 121.4529 Evaluate side-chains 163 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064807 restraints weight = 33111.699| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14193 Z= 0.129 Angle : 0.526 6.785 19318 Z= 0.272 Chirality : 0.044 0.169 2208 Planarity : 0.004 0.046 2482 Dihedral : 4.982 59.187 2004 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.09 % Allowed : 12.91 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1813 helix: 0.68 (0.30), residues: 325 sheet: 0.18 (0.22), residues: 560 loop : 0.18 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 87 TYR 0.014 0.001 TYR C 49 PHE 0.014 0.001 PHE A 104 TRP 0.010 0.001 TRP F 47 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00297 (14172) covalent geometry : angle 0.52390 (19284) SS BOND : bond 0.00174 ( 14) SS BOND : angle 1.01240 ( 28) hydrogen bonds : bond 0.03046 ( 547) hydrogen bonds : angle 5.41895 ( 1542) metal coordination : bond 0.00275 ( 5) link_NAG-ASN : bond 0.00168 ( 2) link_NAG-ASN : angle 1.70328 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 403 ASN cc_start: 0.7828 (m110) cc_final: 0.7565 (m-40) REVERT: B 535 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7242 (mmt) REVERT: C 103 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8079 (tmtt) REVERT: C 207 LYS cc_start: 0.7778 (tppt) cc_final: 0.7114 (mmmt) REVERT: E 32 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8192 (mtt180) REVERT: E 116 PHE cc_start: 0.7583 (m-80) cc_final: 0.7287 (m-80) REVERT: F 67 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8263 (mtm110) outliers start: 31 outliers final: 16 residues processed: 173 average time/residue: 0.6987 time to fit residues: 130.7675 Evaluate side-chains 167 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 166 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 147 GLN F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064806 restraints weight = 32957.533| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.82 r_work: 0.3027 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14193 Z= 0.127 Angle : 0.519 6.437 19318 Z= 0.269 Chirality : 0.044 0.169 2208 Planarity : 0.004 0.046 2482 Dihedral : 4.944 59.330 2004 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.30 % Allowed : 13.45 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1813 helix: 0.72 (0.30), residues: 325 sheet: 0.20 (0.22), residues: 560 loop : 0.16 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 87 TYR 0.015 0.001 TYR C 49 PHE 0.014 0.001 PHE A 104 TRP 0.011 0.001 TRP F 47 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00293 (14172) covalent geometry : angle 0.51724 (19284) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.91616 ( 28) hydrogen bonds : bond 0.02943 ( 547) hydrogen bonds : angle 5.31091 ( 1542) metal coordination : bond 0.00268 ( 5) link_NAG-ASN : bond 0.00182 ( 2) link_NAG-ASN : angle 1.78379 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.535 Fit side-chains REVERT: A 328 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (tpt170) REVERT: A 403 ASN cc_start: 0.7836 (m110) cc_final: 0.7559 (m-40) REVERT: B 448 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 535 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: C 103 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8058 (tmtt) REVERT: C 155 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6657 (mp10) REVERT: C 207 LYS cc_start: 0.7763 (tppt) cc_final: 0.7085 (mmmt) REVERT: D 89 GLU cc_start: 0.7779 (mp0) cc_final: 0.7553 (mp0) REVERT: E 32 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8197 (mtt180) REVERT: E 116 PHE cc_start: 0.7619 (m-80) cc_final: 0.7281 (m-80) outliers start: 34 outliers final: 17 residues processed: 176 average time/residue: 0.6884 time to fit residues: 131.1603 Evaluate side-chains 167 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.078116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063530 restraints weight = 32878.647| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.84 r_work: 0.2988 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14193 Z= 0.187 Angle : 0.565 7.535 19318 Z= 0.291 Chirality : 0.045 0.179 2208 Planarity : 0.004 0.046 2482 Dihedral : 5.102 58.078 2004 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.50 % Allowed : 13.92 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1813 helix: 0.59 (0.29), residues: 325 sheet: 0.09 (0.21), residues: 572 loop : 0.12 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 87 TYR 0.017 0.002 TYR C 49 PHE 0.014 0.002 PHE A 104 TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00440 (14172) covalent geometry : angle 0.56284 (19284) SS BOND : bond 0.00346 ( 14) SS BOND : angle 1.12630 ( 28) hydrogen bonds : bond 0.03237 ( 547) hydrogen bonds : angle 5.42562 ( 1542) metal coordination : bond 0.00432 ( 5) link_NAG-ASN : bond 0.00300 ( 2) link_NAG-ASN : angle 1.97906 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.537 Fit side-chains REVERT: A 58 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8236 (mmt) REVERT: A 403 ASN cc_start: 0.7857 (m110) cc_final: 0.7602 (m-40) REVERT: B 41 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 448 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 535 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7405 (mmt) REVERT: C 103 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8089 (tmtt) REVERT: C 155 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6592 (mp10) REVERT: C 207 LYS cc_start: 0.7783 (tppt) cc_final: 0.7117 (mmmt) REVERT: D 89 GLU cc_start: 0.7829 (mp0) cc_final: 0.7574 (mp0) REVERT: D 220 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7624 (ttm-80) REVERT: E 32 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8216 (mtt180) REVERT: E 107 LYS cc_start: 0.8804 (tptp) cc_final: 0.8318 (tppt) REVERT: E 116 PHE cc_start: 0.7610 (m-80) cc_final: 0.7302 (m-80) REVERT: E 197 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7631 (p) REVERT: F 6 GLU cc_start: 0.8241 (mp0) cc_final: 0.8014 (mp0) outliers start: 37 outliers final: 18 residues processed: 175 average time/residue: 0.7061 time to fit residues: 133.6960 Evaluate side-chains 175 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065787 restraints weight = 31794.788| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.87 r_work: 0.2997 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14193 Z= 0.152 Angle : 0.541 6.614 19318 Z= 0.280 Chirality : 0.045 0.176 2208 Planarity : 0.004 0.048 2482 Dihedral : 4.840 57.743 2000 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.70 % Allowed : 14.12 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1813 helix: 0.63 (0.29), residues: 325 sheet: 0.05 (0.21), residues: 572 loop : 0.11 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 87 TYR 0.017 0.001 TYR C 49 PHE 0.015 0.001 PHE A 104 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00354 (14172) covalent geometry : angle 0.53950 (19284) SS BOND : bond 0.00184 ( 14) SS BOND : angle 0.97290 ( 28) hydrogen bonds : bond 0.03067 ( 547) hydrogen bonds : angle 5.36691 ( 1542) metal coordination : bond 0.00333 ( 5) link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 1.92430 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 403 ASN cc_start: 0.7858 (m110) cc_final: 0.7603 (m-40) REVERT: A 509 GLN cc_start: 0.7841 (tp40) cc_final: 0.7626 (tm-30) REVERT: B 41 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8616 (mp) REVERT: B 448 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: C 155 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: C 207 LYS cc_start: 0.7753 (tppt) cc_final: 0.7010 (mmmt) REVERT: D 89 GLU cc_start: 0.7843 (mp0) cc_final: 0.7547 (mp0) REVERT: D 220 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7578 (ttm-80) REVERT: E 32 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: E 107 LYS cc_start: 0.8804 (tptp) cc_final: 0.8307 (tppt) REVERT: E 116 PHE cc_start: 0.7600 (m-80) cc_final: 0.7295 (m-80) REVERT: E 197 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7600 (p) REVERT: F 3 GLN cc_start: 0.8786 (tt0) cc_final: 0.8428 (tt0) REVERT: F 6 GLU cc_start: 0.8238 (mp0) cc_final: 0.8015 (mp0) outliers start: 40 outliers final: 16 residues processed: 183 average time/residue: 0.6649 time to fit residues: 132.0673 Evaluate side-chains 171 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 156 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN C 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063270 restraints weight = 32641.712| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.81 r_work: 0.2961 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14193 Z= 0.226 Angle : 0.597 7.548 19318 Z= 0.307 Chirality : 0.047 0.185 2208 Planarity : 0.004 0.058 2482 Dihedral : 5.050 57.188 2000 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 15.27 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1813 helix: 0.46 (0.29), residues: 325 sheet: -0.01 (0.21), residues: 582 loop : 0.08 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 87 TYR 0.019 0.002 TYR C 49 PHE 0.014 0.002 PHE A 104 TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00537 (14172) covalent geometry : angle 0.59436 (19284) SS BOND : bond 0.00264 ( 14) SS BOND : angle 1.26308 ( 28) hydrogen bonds : bond 0.03428 ( 547) hydrogen bonds : angle 5.52519 ( 1542) metal coordination : bond 0.00461 ( 5) link_NAG-ASN : bond 0.00418 ( 2) link_NAG-ASN : angle 2.07069 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.555 Fit side-chains REVERT: A 403 ASN cc_start: 0.7914 (m110) cc_final: 0.7671 (m-40) REVERT: B 41 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 224 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: B 448 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: B 480 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8146 (mtp180) REVERT: C 9 SER cc_start: 0.8934 (t) cc_final: 0.8693 (m) REVERT: C 103 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8088 (tmtt) REVERT: C 155 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: C 207 LYS cc_start: 0.7788 (tppt) cc_final: 0.7043 (mmmt) REVERT: D 89 GLU cc_start: 0.7914 (mp0) cc_final: 0.7590 (mp0) REVERT: D 220 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7713 (ttm-80) REVERT: E 32 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8219 (mtt180) REVERT: E 107 LYS cc_start: 0.8809 (tptp) cc_final: 0.8313 (tppt) REVERT: E 116 PHE cc_start: 0.7615 (m-80) cc_final: 0.7298 (m-80) REVERT: F 3 GLN cc_start: 0.8835 (tt0) cc_final: 0.8483 (tt0) REVERT: F 6 GLU cc_start: 0.8322 (mp0) cc_final: 0.8102 (mp0) outliers start: 32 outliers final: 17 residues processed: 180 average time/residue: 0.6736 time to fit residues: 131.0917 Evaluate side-chains 174 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 96 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 179 optimal weight: 0.0060 chunk 92 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.079104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065089 restraints weight = 32386.744| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.80 r_work: 0.3018 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14193 Z= 0.107 Angle : 0.520 5.619 19318 Z= 0.270 Chirality : 0.044 0.164 2208 Planarity : 0.004 0.049 2482 Dihedral : 4.752 57.065 2000 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 15.81 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1813 helix: 0.74 (0.29), residues: 325 sheet: 0.04 (0.21), residues: 570 loop : 0.13 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 87 TYR 0.014 0.001 TYR C 49 PHE 0.017 0.001 PHE A 104 TRP 0.009 0.001 TRP F 47 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00238 (14172) covalent geometry : angle 0.51796 (19284) SS BOND : bond 0.00177 ( 14) SS BOND : angle 0.86578 ( 28) hydrogen bonds : bond 0.02840 ( 547) hydrogen bonds : angle 5.27379 ( 1542) metal coordination : bond 0.00220 ( 5) link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 1.87939 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: A 403 ASN cc_start: 0.7846 (m110) cc_final: 0.7592 (m-40) REVERT: B 448 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 480 ARG cc_start: 0.8378 (mtp180) cc_final: 0.8097 (mtp180) REVERT: C 155 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: C 207 LYS cc_start: 0.7749 (tppt) cc_final: 0.7023 (mmmt) REVERT: D 89 GLU cc_start: 0.7885 (mp0) cc_final: 0.7576 (mp0) REVERT: E 32 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8174 (mtt180) REVERT: E 107 LYS cc_start: 0.8804 (tptp) cc_final: 0.8300 (tppt) REVERT: E 116 PHE cc_start: 0.7620 (m-80) cc_final: 0.7338 (m-80) REVERT: F 3 GLN cc_start: 0.8800 (tt0) cc_final: 0.8449 (tt0) REVERT: F 6 GLU cc_start: 0.8266 (mp0) cc_final: 0.8012 (mp0) outliers start: 27 outliers final: 17 residues processed: 172 average time/residue: 0.6619 time to fit residues: 123.2546 Evaluate side-chains 168 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 159 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 124 GLN C 147 GLN C 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064817 restraints weight = 32717.952| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.81 r_work: 0.3028 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14193 Z= 0.114 Angle : 0.525 6.891 19318 Z= 0.271 Chirality : 0.044 0.160 2208 Planarity : 0.004 0.049 2482 Dihedral : 4.661 56.301 2000 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 15.88 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1813 helix: 0.81 (0.29), residues: 325 sheet: 0.09 (0.21), residues: 578 loop : 0.15 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 87 TYR 0.015 0.001 TYR C 49 PHE 0.016 0.001 PHE A 104 TRP 0.009 0.001 TRP F 47 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00263 (14172) covalent geometry : angle 0.52314 (19284) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.90967 ( 28) hydrogen bonds : bond 0.02846 ( 547) hydrogen bonds : angle 5.20414 ( 1542) metal coordination : bond 0.00177 ( 5) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 1.90985 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 403 ASN cc_start: 0.7853 (m110) cc_final: 0.7588 (m-40) REVERT: B 448 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: B 480 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8094 (mtp180) REVERT: C 155 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6693 (mp10) REVERT: C 207 LYS cc_start: 0.7793 (tppt) cc_final: 0.7064 (mmmt) REVERT: D 89 GLU cc_start: 0.7874 (mp0) cc_final: 0.7549 (mp0) REVERT: E 32 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8169 (mtt180) REVERT: E 107 LYS cc_start: 0.8835 (tptp) cc_final: 0.8349 (tppt) REVERT: E 116 PHE cc_start: 0.7661 (m-80) cc_final: 0.7372 (m-80) REVERT: F 3 GLN cc_start: 0.8779 (tt0) cc_final: 0.8452 (tt0) REVERT: F 6 GLU cc_start: 0.8270 (mp0) cc_final: 0.8016 (mp0) outliers start: 25 outliers final: 16 residues processed: 165 average time/residue: 0.6925 time to fit residues: 123.4935 Evaluate side-chains 163 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS C 147 GLN C 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064835 restraints weight = 31840.256| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.86 r_work: 0.2972 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14193 Z= 0.230 Angle : 0.602 7.483 19318 Z= 0.309 Chirality : 0.047 0.178 2208 Planarity : 0.004 0.051 2482 Dihedral : 5.009 56.600 2000 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.82 % Allowed : 15.81 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1813 helix: 0.54 (0.29), residues: 325 sheet: -0.01 (0.21), residues: 578 loop : 0.09 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 87 TYR 0.021 0.002 TYR C 49 PHE 0.013 0.002 PHE E 139 TRP 0.013 0.002 TRP F 47 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00543 (14172) covalent geometry : angle 0.59921 (19284) SS BOND : bond 0.00294 ( 14) SS BOND : angle 1.32970 ( 28) hydrogen bonds : bond 0.03435 ( 547) hydrogen bonds : angle 5.48771 ( 1542) metal coordination : bond 0.00468 ( 5) link_NAG-ASN : bond 0.00374 ( 2) link_NAG-ASN : angle 2.08901 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.442 Fit side-chains REVERT: A 403 ASN cc_start: 0.7897 (m110) cc_final: 0.7658 (m-40) REVERT: B 224 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 448 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 480 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8142 (mtp180) REVERT: B 535 MET cc_start: 0.7772 (mmm) cc_final: 0.7392 (mmt) REVERT: C 9 SER cc_start: 0.8925 (t) cc_final: 0.8681 (m) REVERT: C 103 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8073 (tmtt) REVERT: C 155 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6616 (mp10) REVERT: C 207 LYS cc_start: 0.7776 (tppt) cc_final: 0.7009 (mmmt) REVERT: D 89 GLU cc_start: 0.7906 (mp0) cc_final: 0.7552 (mp0) REVERT: D 220 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7664 (ttm-80) REVERT: E 32 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8209 (mtt180) REVERT: E 116 PHE cc_start: 0.7618 (m-80) cc_final: 0.7333 (m-80) REVERT: F 3 GLN cc_start: 0.8830 (tt0) cc_final: 0.8494 (tt0) REVERT: F 6 GLU cc_start: 0.8327 (mp0) cc_final: 0.8017 (mp0) REVERT: F 115 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6536 (pm20) outliers start: 27 outliers final: 14 residues processed: 171 average time/residue: 0.6354 time to fit residues: 117.4504 Evaluate side-chains 171 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 147 GLN C 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064077 restraints weight = 32726.628| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.83 r_work: 0.3006 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14193 Z= 0.135 Angle : 0.542 6.491 19318 Z= 0.280 Chirality : 0.045 0.167 2208 Planarity : 0.004 0.051 2482 Dihedral : 4.816 56.626 2000 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.35 % Allowed : 16.28 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1813 helix: 0.71 (0.29), residues: 325 sheet: -0.02 (0.21), residues: 572 loop : 0.13 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 87 TYR 0.015 0.001 TYR C 49 PHE 0.016 0.001 PHE A 104 TRP 0.011 0.001 TRP F 47 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00314 (14172) covalent geometry : angle 0.54038 (19284) SS BOND : bond 0.00156 ( 14) SS BOND : angle 1.03498 ( 28) hydrogen bonds : bond 0.02999 ( 547) hydrogen bonds : angle 5.32046 ( 1542) metal coordination : bond 0.00274 ( 5) link_NAG-ASN : bond 0.00198 ( 2) link_NAG-ASN : angle 1.92763 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4497.26 seconds wall clock time: 77 minutes 30.53 seconds (4650.53 seconds total)