Starting phenix.real_space_refine on Fri Jul 3 13:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590.map" model { file = "/net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24kr_69590/07_2026/24kr_69590_neut.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8841 2.51 5 N 2391 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13938 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3720 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 20, 'TRANS': 477} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 6, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 856 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3720 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 20, 'TRANS': 477} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 6, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 139 Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 856 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3720 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 20, 'TRANS': 477} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 6, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 139 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 856 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ILE A 324 " occ=0.00 ... (3 atoms not shown) pdb=" CB ILE A 324 " occ=0.00 residue: pdb=" N GLN A 325 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN A 325 " occ=0.00 residue: pdb=" N SER A 326 " occ=0.00 ... (3 atoms not shown) pdb=" CB SER A 326 " occ=0.00 residue: pdb=" N ARG A 327 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG A 327 " occ=0.00 residue: pdb=" N GLY A 328 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 328 " occ=0.00 residue: pdb=" N LEU A 329 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU A 329 " occ=0.00 residue: pdb=" N PHE A 330 " occ=0.00 ... (3 atoms not shown) pdb=" CB PHE A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N ILE B 324 " occ=0.00 ... (3 atoms not shown) pdb=" CB ILE B 324 " occ=0.00 residue: pdb=" N GLN B 325 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN B 325 " occ=0.00 residue: pdb=" N SER B 326 " occ=0.00 ... (3 atoms not shown) pdb=" CB SER B 326 " occ=0.00 residue: pdb=" N ARG B 327 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG B 327 " occ=0.00 ... (remaining 12 not shown) Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 13938 At special positions: 0 Unit cell: (109.62, 113.1, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2640 8.00 N 2391 7.00 C 8841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 464 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 464 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " 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 23 " " NAG A 602 " - " ASN A 87 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 287 " " NAG A 605 " - " ASN A 11 " " NAG B 601 " - " ASN B 23 " " NAG B 602 " - " ASN B 87 " " NAG B 603 " - " ASN B 276 " " NAG B 604 " - " ASN B 11 " " NAG B 605 " - " ASN B 287 " " NAG C 601 " - " ASN C 23 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 287 " " NAG C 604 " - " ASN C 87 " " NAG C 605 " - " ASN C 11 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 663.2 milliseconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 42 sheets defined 23.7% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.911A pdb=" N GLU A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 401 through 454 Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.713A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 32 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.909A pdb=" N GLU B 68 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 364 through 385 removed outlier: 4.119A pdb=" N GLU B 374 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 454 Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 485 through 498 removed outlier: 3.715A pdb=" N TYR B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 32 Processing helix chain 'E' and resid 96 through 100A Processing helix chain 'E' and resid 100B through 100F removed outlier: 3.645A pdb=" N ALA E 100E" --> pdb=" O ALA E 100B" (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY E 100F" --> pdb=" O ILE E 100C" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100B through 100F' Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.917A pdb=" N GLU C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'C' and resid 364 through 385 Processing helix chain 'C' and resid 401 through 454 Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 485 through 498 removed outlier: 3.717A pdb=" N TYR C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 100A through 100F removed outlier: 3.736A pdb=" N ALA F 100E" --> pdb=" O ALA F 100B" (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 100F" --> pdb=" O ILE F 100C" (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.382A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 115 removed outlier: 4.087A pdb=" N SER A 110 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 253 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 115 removed outlier: 4.087A pdb=" N SER A 110 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 253 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 138 removed outlier: 7.525A pdb=" N ALA A 135 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ALA A 141 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.684A pdb=" N TYR A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 285 through 286 removed outlier: 3.814A pdb=" N CYS A 279 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB9, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.354A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 108 through 115 removed outlier: 4.125A pdb=" N SER B 110 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR B 253 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 176 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU B 176 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 108 through 115 removed outlier: 4.125A pdb=" N SER B 110 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR B 253 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 176 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 133 through 138 removed outlier: 7.518A pdb=" N ALA B 135 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ALA B 141 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 161 through 166 removed outlier: 3.680A pdb=" N TYR B 206 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 285 through 286 removed outlier: 3.847A pdb=" N CYS B 279 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 457 through 459 Processing sheet with id=AC8, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.672A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.353A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 108 through 115 removed outlier: 4.092A pdb=" N SER C 110 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 253 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU C 176 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU C 176 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 108 through 115 removed outlier: 4.092A pdb=" N SER C 110 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 253 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU C 176 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 138 removed outlier: 7.517A pdb=" N ALA C 135 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ALA C 141 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.616A pdb=" N TYR C 206 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.838A pdb=" N CYS C 279 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 457 through 459 Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.568A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.568A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2253 1.31 - 1.43: 4087 1.43 - 1.56: 7841 1.56 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 14271 Sorted by residual: bond pdb=" C ASP B 373 " pdb=" O ASP B 373 " ideal model delta sigma weight residual 1.234 1.177 0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N ILE B 372 " pdb=" CA ILE B 372 " ideal model delta sigma weight residual 1.462 1.502 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N TYR D 32 " pdb=" CA TYR D 32 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.19e+00 bond pdb=" N VAL D 101 " pdb=" CA VAL D 101 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.38e-02 5.25e+03 8.94e+00 bond pdb=" N TYR F 32 " pdb=" CA TYR F 32 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.80e+00 ... (remaining 14266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 19196 2.21 - 4.42: 221 4.42 - 6.64: 17 6.64 - 8.85: 2 8.85 - 11.06: 4 Bond angle restraints: 19440 Sorted by residual: angle pdb=" C GLU B 374 " pdb=" N ILE B 375 " pdb=" CA ILE B 375 " ideal model delta sigma weight residual 120.46 109.40 11.06 1.37e+00 5.33e-01 6.52e+01 angle pdb=" N ASP B 373 " pdb=" CA ASP B 373 " pdb=" C ASP B 373 " ideal model delta sigma weight residual 110.43 101.18 9.25 1.31e+00 5.83e-01 4.99e+01 angle pdb=" N GLU B 374 " pdb=" CA GLU B 374 " pdb=" CB GLU B 374 " ideal model delta sigma weight residual 110.49 121.09 -10.60 1.69e+00 3.50e-01 3.93e+01 angle pdb=" CA ASP B 373 " pdb=" C ASP B 373 " pdb=" N GLU B 374 " ideal model delta sigma weight residual 115.30 122.55 -7.25 1.33e+00 5.65e-01 2.97e+01 angle pdb=" CA ASP B 373 " pdb=" C ASP B 373 " pdb=" O ASP B 373 " ideal model delta sigma weight residual 121.87 116.76 5.11 1.10e+00 8.26e-01 2.16e+01 ... (remaining 19435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7410 17.78 - 35.56: 831 35.56 - 53.34: 229 53.34 - 71.12: 64 71.12 - 88.90: 19 Dihedral angle restraints: 8553 sinusoidal: 3213 harmonic: 5340 Sorted by residual: dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -167.42 81.42 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS B 90 " pdb=" SG CYS B 90 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -167.02 81.02 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS C 90 " pdb=" SG CYS C 90 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -166.24 80.24 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 8550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1620 0.043 - 0.087: 396 0.087 - 0.130: 162 0.130 - 0.174: 8 0.174 - 0.217: 7 Chirality restraints: 2193 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 11 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU B 374 " pdb=" N GLU B 374 " pdb=" C GLU B 374 " pdb=" CB GLU B 374 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 11 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2190 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 30 " -1.068 9.50e-02 1.11e+02 4.79e-01 1.38e+02 pdb=" NE ARG F 30 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG F 30 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 30 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 30 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 156 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ASN B 156 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN B 156 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B 157 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 156 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C ASN A 156 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 156 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 157 " 0.011 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5930 2.91 - 3.40: 12860 3.40 - 3.90: 24082 3.90 - 4.40: 27330 4.40 - 4.90: 47225 Nonbonded interactions: 117427 Sorted by model distance: nonbonded pdb=" N ASP B 373 " pdb=" O ASP B 373 " model vdw 2.408 2.496 nonbonded pdb=" O ASN B 156 " pdb=" OD1 ASN B 156 " model vdw 2.419 3.040 nonbonded pdb=" O ASN B 370 " pdb=" O ASP B 373 " model vdw 2.438 3.040 nonbonded pdb=" O ASN A 156 " pdb=" OD1 ASN A 156 " model vdw 2.443 3.040 nonbonded pdb=" O ALA B 371 " pdb=" O ASP B 373 " model vdw 2.448 3.040 ... (remaining 117422 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 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 0.057 14307 Z= 0.210 Angle : 0.584 11.059 19527 Z= 0.340 Chirality : 0.044 0.217 2193 Planarity : 0.010 0.479 2493 Dihedral : 16.942 88.901 5094 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % Rotamer: Outliers : 2.75 % Allowed : 26.76 % Favored : 70.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1845 helix: 2.92 (0.25), residues: 375 sheet: -0.55 (0.29), residues: 330 loop : -1.28 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 45 TYR 0.008 0.001 TYR F 90 PHE 0.009 0.001 PHE B 200 TRP 0.008 0.001 TRP D 103 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.21 (14271) covalent geometry : angle 0.57606 / 0.34 (19440) SS BOND : bond 0.00220 / 0.16 ( 21) SS BOND : angle 0.87278 / 0.56 ( 42) hydrogen bonds : bond 0.09510 / 6.81 ( 576) hydrogen bonds : angle 7.11812 / 5.03 ( 1716) link_NAG-ASN : bond 0.00329 / 0.21 ( 15) link_NAG-ASN : angle 1.99476 / 1.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.504 Fit side-chains REVERT: A 16 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8531 (m) REVERT: D 19 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6529 (ptp90) REVERT: D 56 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8171 (t) REVERT: D 83 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7766 (ptmt) REVERT: D 89 MET cc_start: 0.7940 (mmm) cc_final: 0.7660 (tpp) REVERT: B 66 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 235 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8443 (mm-30) REVERT: B 318 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8667 (pp) REVERT: E 6 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: E 19 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6676 (ptp90) REVERT: E 83 LYS cc_start: 0.7993 (ptpp) cc_final: 0.7792 (ptmt) REVERT: E 89 MET cc_start: 0.7941 (mmm) cc_final: 0.7721 (tpp) REVERT: C 235 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8466 (mm-30) REVERT: F 19 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: F 56 SER cc_start: 0.8331 (m) cc_final: 0.8064 (t) REVERT: F 68 THR cc_start: 0.8594 (m) cc_final: 0.8360 (t) REVERT: F 83 LYS cc_start: 0.7930 (ptpp) cc_final: 0.7608 (pttt) REVERT: F 89 MET cc_start: 0.7939 (mmm) cc_final: 0.7681 (tpp) outliers start: 36 outliers final: 15 residues processed: 118 average time/residue: 0.5004 time to fit residues: 65.5290 Evaluate side-chains 101 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 369 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.052610 restraints weight = 31221.937| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.84 r_work: 0.2656 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14307 Z= 0.266 Angle : 0.554 7.736 19527 Z= 0.291 Chirality : 0.046 0.217 2193 Planarity : 0.004 0.040 2493 Dihedral : 6.471 63.413 2357 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.47 % Rotamer: Outliers : 4.43 % Allowed : 24.01 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1845 helix: 2.65 (0.25), residues: 381 sheet: -0.61 (0.28), residues: 342 loop : -1.25 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 30 TYR 0.013 0.001 TYR D 100G PHE 0.014 0.001 PHE B 200 TRP 0.021 0.001 TRP F 103 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (14271) covalent geometry : angle 0.54311 / 0.29 (19440) SS BOND : bond 0.00345 / 0.23 ( 21) SS BOND : angle 0.87173 / 0.57 ( 42) hydrogen bonds : bond 0.04542 / 3.14 ( 576) hydrogen bonds : angle 5.54718 / 3.89 ( 1716) link_NAG-ASN : bond 0.00374 / 0.23 ( 15) link_NAG-ASN : angle 2.19780 / 1.40 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 83 time to evaluate : 0.586 Fit side-chains REVERT: D 19 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6554 (ptp90) REVERT: D 56 SER cc_start: 0.8371 (m) cc_final: 0.8147 (t) REVERT: D 89 MET cc_start: 0.8054 (mmm) cc_final: 0.7694 (tpp) REVERT: B 160 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9011 (tppp) REVERT: B 235 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8437 (mm-30) REVERT: B 318 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8630 (pp) REVERT: E 50 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7481 (ptp-110) REVERT: E 89 MET cc_start: 0.8038 (mmm) cc_final: 0.7741 (tpp) REVERT: C 66 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: C 187 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8318 (t0) REVERT: C 235 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8475 (mm-30) REVERT: C 319 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8165 (mtp85) REVERT: F 19 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6801 (ptp90) REVERT: F 56 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8026 (t) REVERT: F 68 THR cc_start: 0.8655 (m) cc_final: 0.8428 (t) REVERT: F 89 MET cc_start: 0.8027 (mmm) cc_final: 0.7704 (tpp) outliers start: 58 outliers final: 20 residues processed: 132 average time/residue: 0.4357 time to fit residues: 64.7972 Evaluate side-chains 103 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN B 8 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054115 restraints weight = 31174.169| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.85 r_work: 0.2641 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14307 Z= 0.149 Angle : 0.496 6.920 19527 Z= 0.260 Chirality : 0.043 0.211 2193 Planarity : 0.003 0.040 2493 Dihedral : 5.455 54.243 2337 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 25.23 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1845 helix: 2.83 (0.25), residues: 381 sheet: -0.38 (0.28), residues: 330 loop : -1.13 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 30 TYR 0.009 0.001 TYR D 100G PHE 0.009 0.001 PHE C 200 TRP 0.013 0.001 TRP F 103 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14271) covalent geometry : angle 0.48480 / 0.26 (19440) SS BOND : bond 0.00255 / 0.18 ( 21) SS BOND : angle 1.08824 / 0.70 ( 42) hydrogen bonds : bond 0.04018 / 2.76 ( 576) hydrogen bonds : angle 5.13906 / 3.60 ( 1716) link_NAG-ASN : bond 0.00304 / 0.20 ( 15) link_NAG-ASN : angle 2.03528 / 1.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.428 Fit side-chains REVERT: D 50 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7011 (ptp-110) REVERT: D 89 MET cc_start: 0.7991 (mmm) cc_final: 0.7651 (tpp) REVERT: B 160 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8959 (tppp) REVERT: B 235 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8356 (mm-30) REVERT: B 318 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 386 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8842 (tpp) REVERT: E 50 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7687 (ptp-110) REVERT: E 89 MET cc_start: 0.8021 (mmm) cc_final: 0.7771 (tpp) REVERT: C 187 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8261 (t0) REVERT: C 235 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8395 (mm-30) REVERT: F 50 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7133 (ptp-110) REVERT: F 56 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (t) REVERT: F 68 THR cc_start: 0.8590 (m) cc_final: 0.8373 (t) REVERT: F 89 MET cc_start: 0.7974 (mmm) cc_final: 0.7677 (tpp) outliers start: 42 outliers final: 13 residues processed: 125 average time/residue: 0.5117 time to fit residues: 70.3839 Evaluate side-chains 93 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 152 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053715 restraints weight = 31194.857| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.85 r_work: 0.2631 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14307 Z= 0.171 Angle : 0.507 7.518 19527 Z= 0.265 Chirality : 0.043 0.212 2193 Planarity : 0.003 0.042 2493 Dihedral : 5.116 54.460 2318 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 3.98 % Allowed : 25.15 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1845 helix: 2.80 (0.25), residues: 381 sheet: -0.44 (0.27), residues: 342 loop : -1.12 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 217 TYR 0.009 0.001 TYR D 100G PHE 0.011 0.001 PHE C 200 TRP 0.010 0.001 TRP F 103 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14271) covalent geometry : angle 0.49731 / 0.26 (19440) SS BOND : bond 0.00258 / 0.18 ( 21) SS BOND : angle 0.85545 / 0.55 ( 42) hydrogen bonds : bond 0.04045 / 2.77 ( 576) hydrogen bonds : angle 5.05896 / 3.55 ( 1716) link_NAG-ASN : bond 0.00305 / 0.19 ( 15) link_NAG-ASN : angle 2.04179 / 1.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 80 time to evaluate : 0.505 Fit side-chains REVERT: D 50 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7064 (ptp-170) REVERT: D 89 MET cc_start: 0.7942 (mmm) cc_final: 0.7591 (tpp) REVERT: B 160 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8990 (tppp) REVERT: B 235 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8420 (mm-30) REVERT: B 318 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8607 (pp) REVERT: B 386 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8826 (tpp) REVERT: E 6 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: E 50 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7735 (ptp-110) REVERT: E 89 MET cc_start: 0.8006 (mmm) cc_final: 0.7740 (tpp) REVERT: C 235 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8457 (mm-30) REVERT: F 19 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6803 (ptp90) REVERT: F 50 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7222 (ptp-110) REVERT: F 56 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8004 (t) REVERT: F 68 THR cc_start: 0.8637 (m) cc_final: 0.8411 (t) REVERT: F 89 MET cc_start: 0.7958 (mmm) cc_final: 0.7651 (tpp) outliers start: 52 outliers final: 14 residues processed: 122 average time/residue: 0.4562 time to fit residues: 62.3650 Evaluate side-chains 96 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS C 353 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.051295 restraints weight = 31667.078| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.84 r_work: 0.2626 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 14307 Z= 0.354 Angle : 0.613 8.039 19527 Z= 0.319 Chirality : 0.047 0.218 2193 Planarity : 0.004 0.043 2493 Dihedral : 5.888 59.445 2318 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 5.73 % Allowed : 22.78 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1845 helix: 2.42 (0.25), residues: 381 sheet: -0.50 (0.27), residues: 342 loop : -1.24 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 217 TYR 0.013 0.002 TYR D 100G PHE 0.017 0.002 PHE B 200 TRP 0.012 0.001 TRP F 103 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.35 (14271) covalent geometry : angle 0.60200 / 0.32 (19440) SS BOND : bond 0.00436 / 0.29 ( 21) SS BOND : angle 0.96556 / 0.63 ( 42) hydrogen bonds : bond 0.04678 / 3.20 ( 576) hydrogen bonds : angle 5.36912 / 3.78 ( 1716) link_NAG-ASN : bond 0.00470 / 0.30 ( 15) link_NAG-ASN : angle 2.31953 / 1.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 75 time to evaluate : 0.586 Fit side-chains REVERT: D 19 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6920 (ptp90) REVERT: D 50 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7204 (ptp-110) REVERT: D 89 MET cc_start: 0.8163 (mmm) cc_final: 0.7799 (tpp) REVERT: B 66 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: B 160 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9080 (tppp) REVERT: B 235 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8456 (mm-30) REVERT: B 259 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7923 (mpp80) REVERT: B 318 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8558 (pp) REVERT: E 6 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: E 50 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7842 (ptp-110) REVERT: E 89 MET cc_start: 0.8104 (mmm) cc_final: 0.7781 (tpp) REVERT: C 66 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 74 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8586 (t) REVERT: C 235 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8491 (mm-30) REVERT: C 259 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8118 (mpp80) REVERT: F 19 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6814 (ptp90) REVERT: F 50 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7243 (ptp-110) REVERT: F 56 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.8007 (t) REVERT: F 68 THR cc_start: 0.8709 (m) cc_final: 0.8484 (t) REVERT: F 89 MET cc_start: 0.8051 (mmm) cc_final: 0.7686 (tpp) outliers start: 75 outliers final: 26 residues processed: 140 average time/residue: 0.4927 time to fit residues: 76.9979 Evaluate side-chains 111 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN B 194 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054684 restraints weight = 30824.263| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.85 r_work: 0.2700 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14307 Z= 0.116 Angle : 0.491 6.866 19527 Z= 0.257 Chirality : 0.043 0.207 2193 Planarity : 0.003 0.043 2493 Dihedral : 5.090 53.792 2318 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 2.83 % Allowed : 25.54 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 1845 helix: 2.90 (0.25), residues: 381 sheet: -0.32 (0.28), residues: 342 loop : -1.08 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.008 0.001 TYR B 437 PHE 0.008 0.001 PHE B 200 TRP 0.010 0.001 TRP F 103 HIS 0.010 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14271) covalent geometry : angle 0.48032 / 0.25 (19440) SS BOND : bond 0.00212 / 0.17 ( 21) SS BOND : angle 1.13395 / 0.74 ( 42) hydrogen bonds : bond 0.03836 / 2.64 ( 576) hydrogen bonds : angle 4.90627 / 3.43 ( 1716) link_NAG-ASN : bond 0.00293 / 0.19 ( 15) link_NAG-ASN : angle 1.97474 / 1.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.480 Fit side-chains REVERT: D 50 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7093 (ptp-170) REVERT: D 83 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7737 (ptmm) REVERT: D 89 MET cc_start: 0.8057 (mmm) cc_final: 0.7688 (tpp) REVERT: B 235 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8519 (mm-30) REVERT: B 318 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (pp) REVERT: E 6 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: E 19 ARG cc_start: 0.7743 (ppp80) cc_final: 0.7370 (ptt180) REVERT: E 50 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7747 (ptp-110) REVERT: E 89 MET cc_start: 0.8029 (mmm) cc_final: 0.7600 (tpt) REVERT: C 235 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8513 (mm-30) REVERT: F 50 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7273 (ptp-110) REVERT: F 56 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (t) REVERT: F 68 THR cc_start: 0.8679 (m) cc_final: 0.8447 (t) REVERT: F 89 MET cc_start: 0.7986 (mmm) cc_final: 0.7660 (tpp) outliers start: 37 outliers final: 18 residues processed: 118 average time/residue: 0.4770 time to fit residues: 62.5973 Evaluate side-chains 101 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 28 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052605 restraints weight = 31193.183| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.84 r_work: 0.2603 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14307 Z= 0.243 Angle : 0.554 7.330 19527 Z= 0.290 Chirality : 0.045 0.216 2193 Planarity : 0.004 0.043 2493 Dihedral : 5.467 56.117 2318 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.13 % Allowed : 25.38 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1845 helix: 2.69 (0.25), residues: 381 sheet: -0.35 (0.28), residues: 342 loop : -1.17 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.012 0.001 TYR D 100G PHE 0.014 0.001 PHE B 200 TRP 0.010 0.001 TRP F 103 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (14271) covalent geometry : angle 0.54341 / 0.29 (19440) SS BOND : bond 0.00313 / 0.22 ( 21) SS BOND : angle 1.16785 / 0.75 ( 42) hydrogen bonds : bond 0.04281 / 2.93 ( 576) hydrogen bonds : angle 5.09636 / 3.58 ( 1716) link_NAG-ASN : bond 0.00348 / 0.22 ( 15) link_NAG-ASN : angle 2.11244 / 1.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.438 Fit side-chains REVERT: D 50 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7165 (ptp-170) REVERT: D 89 MET cc_start: 0.8095 (mmm) cc_final: 0.7725 (tpp) REVERT: B 160 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9004 (tppp) REVERT: B 235 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8530 (mm-30) REVERT: B 318 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8638 (pp) REVERT: E 6 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: E 50 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7812 (ptp-110) REVERT: E 89 MET cc_start: 0.8039 (mmm) cc_final: 0.7725 (tpp) REVERT: C 74 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8736 (t) REVERT: C 235 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8518 (mm-30) REVERT: F 20 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8374 (mp) REVERT: F 50 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7246 (ptp-110) REVERT: F 56 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8078 (t) REVERT: F 67 PHE cc_start: 0.7851 (m-80) cc_final: 0.7524 (m-80) REVERT: F 83 LYS cc_start: 0.7745 (ptpp) cc_final: 0.7349 (ptmt) REVERT: F 89 MET cc_start: 0.7981 (mmm) cc_final: 0.7639 (tpp) outliers start: 41 outliers final: 21 residues processed: 110 average time/residue: 0.4619 time to fit residues: 56.8019 Evaluate side-chains 105 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 93 optimal weight: 0.3980 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN B 194 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055192 restraints weight = 30851.322| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.84 r_work: 0.2666 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14307 Z= 0.109 Angle : 0.490 9.797 19527 Z= 0.256 Chirality : 0.042 0.206 2193 Planarity : 0.003 0.045 2493 Dihedral : 4.924 53.637 2318 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 2.14 % Allowed : 26.07 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.19), residues: 1845 helix: 3.02 (0.25), residues: 381 sheet: -0.15 (0.28), residues: 342 loop : -1.05 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.011 0.001 TYR A 351 PHE 0.008 0.001 PHE B 200 TRP 0.010 0.001 TRP F 103 HIS 0.005 0.000 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14271) covalent geometry : angle 0.47985 / 0.25 (19440) SS BOND : bond 0.00225 / 0.17 ( 21) SS BOND : angle 1.07009 / 0.68 ( 42) hydrogen bonds : bond 0.03720 / 2.55 ( 576) hydrogen bonds : angle 4.80280 / 3.35 ( 1716) link_NAG-ASN : bond 0.00271 / 0.18 ( 15) link_NAG-ASN : angle 1.88619 / 1.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.542 Fit side-chains REVERT: D 50 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6858 (ptp-170) REVERT: D 83 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7743 (ptmm) REVERT: D 89 MET cc_start: 0.7952 (mmm) cc_final: 0.7545 (tpp) REVERT: B 235 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8462 (mm-30) REVERT: B 318 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8507 (pp) REVERT: E 6 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: E 19 ARG cc_start: 0.7754 (ppp80) cc_final: 0.7392 (ptt180) REVERT: E 50 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7687 (ptp-110) REVERT: E 89 MET cc_start: 0.7982 (mmm) cc_final: 0.7708 (tpp) REVERT: C 235 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8433 (mm-30) REVERT: F 50 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7076 (ptp-110) REVERT: F 83 LYS cc_start: 0.7686 (ptpp) cc_final: 0.7388 (ptmt) REVERT: F 89 MET cc_start: 0.7945 (mmm) cc_final: 0.7632 (tpp) outliers start: 28 outliers final: 13 residues processed: 114 average time/residue: 0.4769 time to fit residues: 60.2936 Evaluate side-chains 96 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 49 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 82AASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 82AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.052192 restraints weight = 31363.825| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.83 r_work: 0.2593 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 14307 Z= 0.282 Angle : 0.582 9.364 19527 Z= 0.303 Chirality : 0.045 0.214 2193 Planarity : 0.004 0.043 2493 Dihedral : 5.574 56.846 2318 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 2.37 % Allowed : 25.92 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1845 helix: 2.68 (0.25), residues: 381 sheet: -0.21 (0.28), residues: 342 loop : -1.15 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 259 TYR 0.014 0.002 TYR D 100G PHE 0.014 0.002 PHE B 200 TRP 0.008 0.001 TRP F 103 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (14271) covalent geometry : angle 0.57150 / 0.30 (19440) SS BOND : bond 0.00339 / 0.23 ( 21) SS BOND : angle 1.10732 / 0.71 ( 42) hydrogen bonds : bond 0.04394 / 3.00 ( 576) hydrogen bonds : angle 5.10764 / 3.58 ( 1716) link_NAG-ASN : bond 0.00379 / 0.24 ( 15) link_NAG-ASN : angle 2.13811 / 1.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.553 Fit side-chains REVERT: D 50 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7179 (ptp-110) REVERT: D 83 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7669 (ptmm) REVERT: D 89 MET cc_start: 0.8073 (mmm) cc_final: 0.7705 (tpp) REVERT: B 66 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: B 235 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8506 (mm-30) REVERT: B 318 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8620 (pp) REVERT: E 6 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: E 50 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7743 (ptp-110) REVERT: E 89 MET cc_start: 0.8063 (mmm) cc_final: 0.7721 (tpp) REVERT: C 235 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8517 (mm-30) REVERT: F 50 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7243 (ptp-110) REVERT: F 67 PHE cc_start: 0.7911 (m-80) cc_final: 0.7613 (m-10) REVERT: F 89 MET cc_start: 0.8019 (mmm) cc_final: 0.7665 (tpp) outliers start: 31 outliers final: 19 residues processed: 101 average time/residue: 0.4708 time to fit residues: 53.2407 Evaluate side-chains 98 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.074369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053412 restraints weight = 30917.443| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.84 r_work: 0.2624 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14307 Z= 0.177 Angle : 0.530 9.298 19527 Z= 0.278 Chirality : 0.043 0.209 2193 Planarity : 0.004 0.045 2493 Dihedral : 5.293 54.942 2318 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 1.99 % Allowed : 26.61 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1845 helix: 2.83 (0.25), residues: 381 sheet: -0.16 (0.28), residues: 342 loop : -1.08 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.011 0.001 TYR A 351 PHE 0.012 0.001 PHE F 67 TRP 0.010 0.001 TRP F 103 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (14271) covalent geometry : angle 0.51981 / 0.28 (19440) SS BOND : bond 0.00248 / 0.18 ( 21) SS BOND : angle 1.09696 / 0.70 ( 42) hydrogen bonds : bond 0.04050 / 2.77 ( 576) hydrogen bonds : angle 4.96061 / 3.47 ( 1716) link_NAG-ASN : bond 0.00302 / 0.19 ( 15) link_NAG-ASN : angle 2.02102 / 1.29 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.603 Fit side-chains REVERT: D 19 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6699 (ptp90) REVERT: D 50 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: D 83 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7737 (ptmm) REVERT: D 89 MET cc_start: 0.8015 (mmm) cc_final: 0.7576 (tpp) REVERT: B 66 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: B 235 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8542 (mm-30) REVERT: B 318 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8663 (pp) REVERT: E 6 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: E 19 ARG cc_start: 0.7831 (ppp80) cc_final: 0.7481 (ptt180) REVERT: E 50 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7790 (ptp-110) REVERT: E 89 MET cc_start: 0.8061 (mmm) cc_final: 0.7743 (tpp) REVERT: C 66 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 235 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8531 (mm-30) REVERT: F 50 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7247 (ptp-110) REVERT: F 83 LYS cc_start: 0.7704 (ptpp) cc_final: 0.7301 (ptmt) REVERT: F 89 MET cc_start: 0.7979 (mmm) cc_final: 0.7645 (tpp) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.5248 time to fit residues: 58.9863 Evaluate side-chains 98 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 5 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82AASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82AASN C 8 HIS ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054154 restraints weight = 30973.796| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.84 r_work: 0.2641 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14307 Z= 0.145 Angle : 0.518 9.215 19527 Z= 0.272 Chirality : 0.043 0.207 2193 Planarity : 0.004 0.044 2493 Dihedral : 5.115 53.658 2318 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 1.99 % Allowed : 26.61 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1845 helix: 2.95 (0.25), residues: 381 sheet: -0.11 (0.28), residues: 342 loop : -1.02 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.011 0.001 TYR A 351 PHE 0.015 0.001 PHE F 67 TRP 0.011 0.001 TRP F 103 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14271) covalent geometry : angle 0.50912 / 0.27 (19440) SS BOND : bond 0.00240 / 0.18 ( 21) SS BOND : angle 0.98280 / 0.63 ( 42) hydrogen bonds : bond 0.03901 / 2.67 ( 576) hydrogen bonds : angle 4.87685 / 3.41 ( 1716) link_NAG-ASN : bond 0.00277 / 0.18 ( 15) link_NAG-ASN : angle 1.92274 / 1.22 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4033.66 seconds wall clock time: 69 minutes 37.21 seconds (4177.21 seconds total)