Starting phenix.real_space_refine on Thu Feb 5 09:36:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh6_63086/02_2026/9lh6_63086.map" } resolution = 2.69 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= 0.066 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 115 5.16 5 C 10560 2.51 5 N 2610 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16235 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 3.78, per 1000 atoms: 0.23 Number of scatterers: 16235 At special positions: 0 Unit cell: (91.91, 91.91, 168.67, 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 115 16.00 O 2950 8.00 N 2610 7.00 C 10560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 602 " - " ASN C 46 " " NAG D 602 " - " ASN D 46 " " NAG E 602 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 43.3% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.671A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.572A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.821A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.372A pdb=" N CYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 490 removed outlier: 4.189A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.672A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.571A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 260 through 281 removed outlier: 3.821A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 343 removed outlier: 4.372A pdb=" N CYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 490 removed outlier: 4.189A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.671A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.571A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.821A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 343 removed outlier: 4.372A pdb=" N CYS C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 490 removed outlier: 4.189A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.671A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.571A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 260 through 281 removed outlier: 3.820A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 343 removed outlier: 4.371A pdb=" N CYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 490 removed outlier: 4.189A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.671A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 249 removed outlier: 3.572A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 260 through 281 removed outlier: 3.821A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 343 removed outlier: 4.372A pdb=" N CYS E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 490 removed outlier: 4.189A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.540A pdb=" N ILE A 76 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 144 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.803A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.541A pdb=" N ILE B 76 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 144 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.803A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN B 79 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER B 58 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER B 56 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR B 83 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N TYR B 54 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.585A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.585A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.540A pdb=" N ILE C 76 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 144 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.803A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN C 79 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER C 58 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER C 56 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR C 83 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N TYR C 54 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.540A pdb=" N ILE D 76 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 144 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.804A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN D 79 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER D 58 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER D 81 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER D 56 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR D 83 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N TYR D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.540A pdb=" N ILE E 76 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 144 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.803A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.584A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2733 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: 2.99 Time building geometry restraints manager: 2.08 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: 2570 1.31 - 1.44: 4650 1.44 - 1.57: 9280 1.57 - 1.70: 10 1.70 - 1.83: 170 Bond restraints: 16680 Sorted by residual: bond pdb=" C6 NCT E 601 " pdb=" N2 NCT E 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.623 -0.171 2.00e-02 2.50e+03 7.35e+01 ... (remaining 16675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 22240 1.92 - 3.83: 390 3.83 - 5.75: 105 5.75 - 7.67: 10 7.67 - 9.59: 10 Bond angle restraints: 22755 Sorted by residual: angle pdb=" CA TRP C 341 " pdb=" CB TRP C 341 " pdb=" CG TRP C 341 " ideal model delta sigma weight residual 113.60 119.90 -6.30 1.90e+00 2.77e-01 1.10e+01 angle pdb=" CA TRP B 341 " pdb=" CB TRP B 341 " pdb=" CG TRP B 341 " ideal model delta sigma weight residual 113.60 119.88 -6.28 1.90e+00 2.77e-01 1.09e+01 angle pdb=" CA TRP A 341 " pdb=" CB TRP A 341 " pdb=" CG TRP A 341 " ideal model delta sigma weight residual 113.60 119.88 -6.28 1.90e+00 2.77e-01 1.09e+01 angle pdb=" CA TRP E 341 " pdb=" CB TRP E 341 " pdb=" CG TRP E 341 " ideal model delta sigma weight residual 113.60 119.87 -6.27 1.90e+00 2.77e-01 1.09e+01 angle pdb=" CA TRP D 341 " pdb=" CB TRP D 341 " pdb=" CG TRP D 341 " ideal model delta sigma weight residual 113.60 119.86 -6.26 1.90e+00 2.77e-01 1.08e+01 ... (remaining 22750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 8638 16.42 - 32.84: 1022 32.84 - 49.26: 295 49.26 - 65.67: 80 65.67 - 82.09: 35 Dihedral angle restraints: 10070 sinusoidal: 4175 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " pdb=" SG CYS D 164 " pdb=" CB CYS D 164 " ideal model delta sinusoidal sigma weight residual 93.00 49.38 43.62 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 49.38 43.62 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 49.38 43.62 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 10067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2033 0.046 - 0.093: 454 0.093 - 0.139: 88 0.139 - 0.186: 20 0.186 - 0.232: 10 Chirality restraints: 2605 Sorted by residual: chirality pdb=" C4 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" C5 NAG I 1 " pdb=" O4 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2602 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 334 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ILE D 334 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE D 334 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU D 335 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 334 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ILE B 334 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE B 334 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 335 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 334 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ILE A 334 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 334 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 335 " -0.009 2.00e-02 2.50e+03 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6425 2.91 - 3.41: 14584 3.41 - 3.90: 26919 3.90 - 4.40: 29751 4.40 - 4.90: 51292 Nonbonded interactions: 128971 Sorted by model distance: nonbonded pdb=" OG SER C 81 " pdb=" NE2BHIS C 137 " model vdw 2.410 3.120 nonbonded pdb=" O VAL E 304 " pdb=" OG SER E 307 " model vdw 2.423 3.040 nonbonded pdb=" O VAL C 304 " pdb=" OG SER C 307 " model vdw 2.423 3.040 nonbonded pdb=" O VAL B 304 " pdb=" OG SER B 307 " model vdw 2.423 3.040 nonbonded pdb=" O VAL A 304 " pdb=" OG SER A 307 " model vdw 2.423 3.040 ... (remaining 128966 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.050 Set scattering table: 0.040 Process input model: 17.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 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 : 0.009 0.173 16705 Z= 0.421 Angle : 0.671 9.586 22820 Z= 0.309 Chirality : 0.044 0.232 2605 Planarity : 0.004 0.037 2835 Dihedral : 16.318 82.093 6230 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.74 % Allowed : 17.11 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.08 (0.18), residues: 1985 helix: 2.98 (0.17), residues: 820 sheet: 0.66 (0.24), residues: 455 loop : -0.04 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.008 0.001 TYR B 233 PHE 0.008 0.001 PHE C 275 TRP 0.007 0.001 TRP C 341 HIS 0.003 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00857 (16680) covalent geometry : angle 0.65869 (22755) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.42353 ( 20) hydrogen bonds : bond 0.12694 ( 846) hydrogen bonds : angle 5.63011 ( 2733) link_BETA1-4 : bond 0.00238 ( 5) link_BETA1-4 : angle 1.31945 ( 15) link_NAG-ASN : bond 0.00188 ( 10) link_NAG-ASN : angle 3.30947 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 266 time to evaluate : 0.658 Fit side-chains REVERT: A 321 ASP cc_start: 0.9016 (t0) cc_final: 0.8717 (t0) REVERT: A 342 PHE cc_start: 0.9034 (t80) cc_final: 0.7735 (m-10) REVERT: A 435 LYS cc_start: 0.8979 (mttt) cc_final: 0.7708 (mttt) REVERT: A 439 GLU cc_start: 0.9233 (mm-30) cc_final: 0.7918 (mp0) REVERT: A 476 SER cc_start: 0.9494 (t) cc_final: 0.9105 (p) REVERT: B 236 ASN cc_start: 0.9028 (m110) cc_final: 0.8656 (m-40) REVERT: B 321 ASP cc_start: 0.8914 (t0) cc_final: 0.8583 (t0) REVERT: B 435 LYS cc_start: 0.9024 (mttt) cc_final: 0.8548 (mttm) REVERT: B 439 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 454 GLU cc_start: 0.8612 (pt0) cc_final: 0.8383 (pp20) REVERT: B 476 SER cc_start: 0.9542 (t) cc_final: 0.9133 (p) REVERT: C 321 ASP cc_start: 0.8931 (t0) cc_final: 0.8452 (t0) REVERT: C 435 LYS cc_start: 0.9005 (mttt) cc_final: 0.7919 (mttt) REVERT: C 437 LEU cc_start: 0.9315 (tp) cc_final: 0.9063 (tt) REVERT: C 439 GLU cc_start: 0.9253 (mm-30) cc_final: 0.7999 (mp0) REVERT: C 476 SER cc_start: 0.9552 (t) cc_final: 0.9158 (p) REVERT: D 321 ASP cc_start: 0.9034 (t0) cc_final: 0.8696 (t0) REVERT: D 435 LYS cc_start: 0.8984 (mttt) cc_final: 0.8305 (mttm) REVERT: D 439 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8709 (mm-30) REVERT: D 454 GLU cc_start: 0.8574 (pt0) cc_final: 0.8362 (pp20) REVERT: D 476 SER cc_start: 0.9494 (t) cc_final: 0.9169 (p) REVERT: E 226 MET cc_start: 0.9328 (ptp) cc_final: 0.9090 (ptm) REVERT: E 321 ASP cc_start: 0.8916 (t0) cc_final: 0.8491 (t0) REVERT: E 435 LYS cc_start: 0.9043 (mttt) cc_final: 0.7812 (mttp) REVERT: E 439 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8467 (mm-30) REVERT: E 454 GLU cc_start: 0.8571 (pt0) cc_final: 0.8349 (pp20) REVERT: E 476 SER cc_start: 0.9530 (t) cc_final: 0.9286 (p) outliers start: 13 outliers final: 10 residues processed: 276 average time/residue: 0.5080 time to fit residues: 159.3931 Evaluate side-chains 213 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 274 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.061963 restraints weight = 73381.395| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.06 r_work: 0.2570 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16705 Z= 0.151 Angle : 0.633 9.776 22820 Z= 0.307 Chirality : 0.045 0.412 2605 Planarity : 0.004 0.038 2835 Dihedral : 8.341 45.194 2555 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.72 % Allowed : 17.56 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.00 (0.18), residues: 1985 helix: 2.90 (0.17), residues: 820 sheet: 0.51 (0.26), residues: 405 loop : 0.06 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.008 0.001 TYR D 233 PHE 0.010 0.001 PHE A 478 TRP 0.013 0.001 TRP E 82 HIS 0.002 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00337 (16680) covalent geometry : angle 0.60410 (22755) SS BOND : bond 0.00887 ( 10) SS BOND : angle 1.91064 ( 20) hydrogen bonds : bond 0.05606 ( 846) hydrogen bonds : angle 4.03400 ( 2733) link_BETA1-4 : bond 0.00255 ( 5) link_BETA1-4 : angle 2.81004 ( 15) link_NAG-ASN : bond 0.00345 ( 10) link_NAG-ASN : angle 4.63506 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.701 Fit side-chains REVERT: A 321 ASP cc_start: 0.9095 (t0) cc_final: 0.8772 (t0) REVERT: A 342 PHE cc_start: 0.8897 (t80) cc_final: 0.7623 (m-10) REVERT: A 435 LYS cc_start: 0.8529 (mttt) cc_final: 0.7766 (mttt) REVERT: A 438 GLU cc_start: 0.8215 (pp20) cc_final: 0.7351 (pp20) REVERT: A 439 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8547 (mp0) REVERT: B 236 ASN cc_start: 0.8765 (m110) cc_final: 0.8270 (m110) REVERT: B 321 ASP cc_start: 0.9004 (t0) cc_final: 0.8565 (t0) REVERT: B 345 MET cc_start: 0.8676 (mmt) cc_final: 0.8449 (mmm) REVERT: B 435 LYS cc_start: 0.8685 (mttt) cc_final: 0.7932 (mttp) REVERT: B 438 GLU cc_start: 0.8108 (pp20) cc_final: 0.7339 (pp20) REVERT: B 439 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8644 (mp0) REVERT: B 454 GLU cc_start: 0.8613 (pt0) cc_final: 0.8306 (pp20) REVERT: B 476 SER cc_start: 0.9092 (t) cc_final: 0.8880 (p) REVERT: C 321 ASP cc_start: 0.9050 (t0) cc_final: 0.8516 (t0) REVERT: C 342 PHE cc_start: 0.8338 (t80) cc_final: 0.7466 (m-10) REVERT: C 345 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8206 (mmt) REVERT: C 435 LYS cc_start: 0.8693 (mttt) cc_final: 0.8052 (mttt) REVERT: C 438 GLU cc_start: 0.8089 (pp20) cc_final: 0.7297 (pp20) REVERT: C 439 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8497 (mp0) REVERT: C 476 SER cc_start: 0.9136 (t) cc_final: 0.8902 (p) REVERT: D 321 ASP cc_start: 0.9108 (t0) cc_final: 0.8755 (t0) REVERT: D 435 LYS cc_start: 0.8568 (mttt) cc_final: 0.8058 (mttm) REVERT: D 438 GLU cc_start: 0.8030 (pp20) cc_final: 0.7318 (pp20) REVERT: D 439 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8593 (mp0) REVERT: D 454 GLU cc_start: 0.8624 (pt0) cc_final: 0.8348 (pp20) REVERT: D 476 SER cc_start: 0.9148 (t) cc_final: 0.8652 (p) REVERT: E 275 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7556 (t80) REVERT: E 321 ASP cc_start: 0.9038 (t0) cc_final: 0.8583 (t0) REVERT: E 435 LYS cc_start: 0.8567 (mttt) cc_final: 0.7800 (mttt) REVERT: E 438 GLU cc_start: 0.8005 (pp20) cc_final: 0.7003 (pp20) REVERT: E 439 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8619 (mp0) REVERT: E 454 GLU cc_start: 0.8593 (pt0) cc_final: 0.8327 (pp20) REVERT: E 476 SER cc_start: 0.9125 (t) cc_final: 0.8919 (p) outliers start: 48 outliers final: 14 residues processed: 246 average time/residue: 0.5024 time to fit residues: 140.6275 Evaluate side-chains 226 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 0.0030 chunk 14 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.061180 restraints weight = 57611.660| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.57 r_work: 0.2545 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16705 Z= 0.133 Angle : 0.603 10.304 22820 Z= 0.291 Chirality : 0.045 0.468 2605 Planarity : 0.004 0.036 2835 Dihedral : 6.760 38.869 2545 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.10 % Allowed : 17.68 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.05 (0.18), residues: 1985 helix: 2.88 (0.17), residues: 820 sheet: 0.61 (0.25), residues: 405 loop : 0.12 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 121 TYR 0.006 0.001 TYR D 233 PHE 0.011 0.001 PHE E 462 TRP 0.009 0.001 TRP D 82 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00296 (16680) covalent geometry : angle 0.56959 (22755) SS BOND : bond 0.00797 ( 10) SS BOND : angle 1.43341 ( 20) hydrogen bonds : bond 0.05345 ( 846) hydrogen bonds : angle 3.89397 ( 2733) link_BETA1-4 : bond 0.00229 ( 5) link_BETA1-4 : angle 2.84162 ( 15) link_NAG-ASN : bond 0.00261 ( 10) link_NAG-ASN : angle 4.98620 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.736 Fit side-chains REVERT: A 321 ASP cc_start: 0.9132 (t0) cc_final: 0.8812 (t0) REVERT: A 342 PHE cc_start: 0.8909 (t80) cc_final: 0.7681 (m-10) REVERT: A 435 LYS cc_start: 0.8501 (mttt) cc_final: 0.7422 (mttt) REVERT: A 438 GLU cc_start: 0.8200 (pp20) cc_final: 0.7440 (pp20) REVERT: A 439 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8490 (mp0) REVERT: B 236 ASN cc_start: 0.8643 (m110) cc_final: 0.8295 (m-40) REVERT: B 321 ASP cc_start: 0.8986 (t0) cc_final: 0.8538 (t0) REVERT: B 435 LYS cc_start: 0.8693 (mttt) cc_final: 0.8115 (mttp) REVERT: B 438 GLU cc_start: 0.8062 (pp20) cc_final: 0.7229 (pp20) REVERT: B 439 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8560 (mp0) REVERT: B 454 GLU cc_start: 0.8549 (pt0) cc_final: 0.8256 (pp20) REVERT: B 476 SER cc_start: 0.9032 (t) cc_final: 0.8823 (p) REVERT: C 321 ASP cc_start: 0.9004 (t0) cc_final: 0.8486 (t0) REVERT: C 342 PHE cc_start: 0.8326 (t80) cc_final: 0.7423 (m-10) REVERT: C 435 LYS cc_start: 0.8633 (mttt) cc_final: 0.7822 (mttt) REVERT: C 438 GLU cc_start: 0.8032 (pp20) cc_final: 0.7167 (pp20) REVERT: C 439 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8379 (mp0) REVERT: C 476 SER cc_start: 0.9079 (t) cc_final: 0.8853 (p) REVERT: C 478 PHE cc_start: 0.8395 (t80) cc_final: 0.8142 (t80) REVERT: D 197 ASP cc_start: 0.8756 (t70) cc_final: 0.8259 (t0) REVERT: D 321 ASP cc_start: 0.9077 (t0) cc_final: 0.8678 (t0) REVERT: D 435 LYS cc_start: 0.8545 (mttt) cc_final: 0.8079 (mttm) REVERT: D 438 GLU cc_start: 0.7947 (pp20) cc_final: 0.7746 (pp20) REVERT: D 439 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8912 (mm-30) REVERT: D 454 GLU cc_start: 0.8584 (pt0) cc_final: 0.8299 (pp20) REVERT: E 275 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7516 (t80) REVERT: E 321 ASP cc_start: 0.9021 (t0) cc_final: 0.8575 (t0) REVERT: E 435 LYS cc_start: 0.8527 (mttt) cc_final: 0.8013 (mttp) REVERT: E 438 GLU cc_start: 0.7987 (pp20) cc_final: 0.7586 (pp20) REVERT: E 439 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8845 (mm-30) REVERT: E 454 GLU cc_start: 0.8524 (pt0) cc_final: 0.8224 (pp20) REVERT: E 476 SER cc_start: 0.9074 (t) cc_final: 0.8870 (p) outliers start: 37 outliers final: 16 residues processed: 239 average time/residue: 0.4630 time to fit residues: 126.7172 Evaluate side-chains 234 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 133 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.062643 restraints weight = 69258.741| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.90 r_work: 0.2573 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16705 Z= 0.150 Angle : 0.600 10.798 22820 Z= 0.291 Chirality : 0.045 0.491 2605 Planarity : 0.004 0.035 2835 Dihedral : 6.417 33.857 2545 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.98 % Allowed : 18.13 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.04 (0.18), residues: 1985 helix: 2.84 (0.17), residues: 820 sheet: 0.56 (0.25), residues: 405 loop : 0.18 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.007 0.001 TYR D 233 PHE 0.008 0.001 PHE E 462 TRP 0.008 0.001 TRP D 82 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00344 (16680) covalent geometry : angle 0.56394 (22755) SS BOND : bond 0.00775 ( 10) SS BOND : angle 1.46358 ( 20) hydrogen bonds : bond 0.05343 ( 846) hydrogen bonds : angle 3.92178 ( 2733) link_BETA1-4 : bond 0.00186 ( 5) link_BETA1-4 : angle 2.77570 ( 15) link_NAG-ASN : bond 0.00193 ( 10) link_NAG-ASN : angle 5.19348 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.779 Fit side-chains REVERT: A 321 ASP cc_start: 0.9153 (t0) cc_final: 0.8848 (t0) REVERT: A 342 PHE cc_start: 0.8954 (t80) cc_final: 0.7713 (m-10) REVERT: A 435 LYS cc_start: 0.8564 (mttt) cc_final: 0.7376 (mttt) REVERT: A 438 GLU cc_start: 0.8257 (pp20) cc_final: 0.7467 (pp20) REVERT: A 439 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8511 (mp0) REVERT: B 321 ASP cc_start: 0.9011 (t0) cc_final: 0.8561 (t0) REVERT: B 435 LYS cc_start: 0.8694 (mttt) cc_final: 0.8299 (mttp) REVERT: B 438 GLU cc_start: 0.8147 (pp20) cc_final: 0.7857 (pp20) REVERT: B 439 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8906 (mm-30) REVERT: B 454 GLU cc_start: 0.8618 (pt0) cc_final: 0.8311 (pp20) REVERT: B 476 SER cc_start: 0.9106 (t) cc_final: 0.8884 (p) REVERT: C 197 ASP cc_start: 0.8646 (t70) cc_final: 0.8215 (t0) REVERT: C 321 ASP cc_start: 0.9052 (t0) cc_final: 0.8527 (t0) REVERT: C 342 PHE cc_start: 0.8323 (t80) cc_final: 0.7427 (m-10) REVERT: C 435 LYS cc_start: 0.8682 (mttt) cc_final: 0.7871 (mttt) REVERT: C 438 GLU cc_start: 0.8110 (pp20) cc_final: 0.7164 (pp20) REVERT: C 439 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8369 (mp0) REVERT: C 476 SER cc_start: 0.9149 (t) cc_final: 0.8914 (p) REVERT: D 197 ASP cc_start: 0.8763 (t70) cc_final: 0.8302 (t0) REVERT: D 321 ASP cc_start: 0.9124 (t0) cc_final: 0.8758 (t0) REVERT: D 435 LYS cc_start: 0.8617 (mttt) cc_final: 0.7886 (mttm) REVERT: D 438 GLU cc_start: 0.8010 (pp20) cc_final: 0.7149 (pp20) REVERT: D 439 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8481 (mp0) REVERT: D 454 GLU cc_start: 0.8634 (pt0) cc_final: 0.8345 (pp20) REVERT: E 275 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7546 (t80) REVERT: E 321 ASP cc_start: 0.9095 (t0) cc_final: 0.8668 (t0) REVERT: E 435 LYS cc_start: 0.8604 (mttt) cc_final: 0.7730 (mttp) REVERT: E 438 GLU cc_start: 0.8040 (pp20) cc_final: 0.7021 (pp20) REVERT: E 439 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8582 (mp0) REVERT: E 454 GLU cc_start: 0.8592 (pt0) cc_final: 0.8279 (pp20) REVERT: E 473 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: E 476 SER cc_start: 0.9157 (t) cc_final: 0.8771 (p) outliers start: 35 outliers final: 16 residues processed: 237 average time/residue: 0.4500 time to fit residues: 122.3642 Evaluate side-chains 238 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Chi-restraints excluded: chain E residue 473 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.063805 restraints weight = 49848.568| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.31 r_work: 0.2586 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16705 Z= 0.110 Angle : 0.579 10.764 22820 Z= 0.279 Chirality : 0.045 0.498 2605 Planarity : 0.004 0.034 2835 Dihedral : 6.197 32.502 2545 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.47 % Allowed : 19.32 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.14 (0.18), residues: 1985 helix: 2.93 (0.17), residues: 815 sheet: 0.66 (0.25), residues: 405 loop : 0.22 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.005 0.001 TYR E 232 PHE 0.007 0.001 PHE E 462 TRP 0.007 0.001 TRP E 82 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00237 (16680) covalent geometry : angle 0.54121 (22755) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.44946 ( 20) hydrogen bonds : bond 0.04924 ( 846) hydrogen bonds : angle 3.75183 ( 2733) link_BETA1-4 : bond 0.00120 ( 5) link_BETA1-4 : angle 2.82349 ( 15) link_NAG-ASN : bond 0.00405 ( 10) link_NAG-ASN : angle 5.27707 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.676 Fit side-chains REVERT: A 197 ASP cc_start: 0.8645 (t70) cc_final: 0.8188 (t0) REVERT: A 321 ASP cc_start: 0.9139 (t0) cc_final: 0.8828 (t0) REVERT: A 342 PHE cc_start: 0.8950 (t80) cc_final: 0.7687 (m-10) REVERT: A 435 LYS cc_start: 0.8555 (mttt) cc_final: 0.7228 (mttt) REVERT: A 438 GLU cc_start: 0.8188 (pp20) cc_final: 0.7429 (pp20) REVERT: A 439 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8378 (mp0) REVERT: B 197 ASP cc_start: 0.8597 (t70) cc_final: 0.8110 (t0) REVERT: B 257 ASP cc_start: 0.8941 (m-30) cc_final: 0.8669 (m-30) REVERT: B 283 MET cc_start: 0.8893 (mmm) cc_final: 0.8587 (mmp) REVERT: B 321 ASP cc_start: 0.8984 (t0) cc_final: 0.8546 (t0) REVERT: B 435 LYS cc_start: 0.8646 (mttt) cc_final: 0.8266 (mttp) REVERT: B 438 GLU cc_start: 0.8120 (pp20) cc_final: 0.7814 (pp20) REVERT: B 439 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 454 GLU cc_start: 0.8504 (pt0) cc_final: 0.8242 (pp20) REVERT: B 476 SER cc_start: 0.9047 (t) cc_final: 0.8827 (p) REVERT: C 197 ASP cc_start: 0.8554 (t70) cc_final: 0.8106 (t0) REVERT: C 321 ASP cc_start: 0.9004 (t0) cc_final: 0.8480 (t0) REVERT: C 342 PHE cc_start: 0.8290 (t80) cc_final: 0.7401 (m-10) REVERT: C 435 LYS cc_start: 0.8653 (mttt) cc_final: 0.7686 (mttt) REVERT: C 438 GLU cc_start: 0.8074 (pp20) cc_final: 0.7267 (pp20) REVERT: C 439 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8295 (mp0) REVERT: C 476 SER cc_start: 0.9111 (t) cc_final: 0.8871 (p) REVERT: C 478 PHE cc_start: 0.8375 (t80) cc_final: 0.8146 (t80) REVERT: D 197 ASP cc_start: 0.8720 (t70) cc_final: 0.8255 (t0) REVERT: D 321 ASP cc_start: 0.9056 (t0) cc_final: 0.8650 (t0) REVERT: D 435 LYS cc_start: 0.8618 (mttt) cc_final: 0.8092 (mttm) REVERT: D 438 GLU cc_start: 0.7995 (pp20) cc_final: 0.7781 (pp20) REVERT: D 439 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8879 (mm-30) REVERT: D 454 GLU cc_start: 0.8555 (pt0) cc_final: 0.8258 (pp20) REVERT: E 197 ASP cc_start: 0.8612 (t70) cc_final: 0.8151 (t0) REVERT: E 275 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7433 (t80) REVERT: E 321 ASP cc_start: 0.9032 (t0) cc_final: 0.8586 (t0) REVERT: E 435 LYS cc_start: 0.8563 (mttt) cc_final: 0.7545 (mttp) REVERT: E 438 GLU cc_start: 0.8033 (pp20) cc_final: 0.6997 (pp20) REVERT: E 439 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8538 (mp0) REVERT: E 454 GLU cc_start: 0.8492 (pt0) cc_final: 0.8172 (pp20) REVERT: E 476 SER cc_start: 0.9032 (t) cc_final: 0.8829 (p) outliers start: 26 outliers final: 16 residues processed: 244 average time/residue: 0.4384 time to fit residues: 123.0645 Evaluate side-chains 238 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 22 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.061566 restraints weight = 63254.408| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.73 r_work: 0.2555 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16705 Z= 0.199 Angle : 0.627 11.474 22820 Z= 0.304 Chirality : 0.047 0.538 2605 Planarity : 0.004 0.033 2835 Dihedral : 5.941 33.980 2545 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.64 % Allowed : 19.43 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.08 (0.18), residues: 1985 helix: 2.79 (0.17), residues: 820 sheet: 0.73 (0.24), residues: 445 loop : 0.19 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.009 0.001 TYR D 296 PHE 0.009 0.001 PHE C 157 TRP 0.009 0.001 TRP E 341 HIS 0.003 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00465 (16680) covalent geometry : angle 0.59062 (22755) SS BOND : bond 0.00775 ( 10) SS BOND : angle 1.46087 ( 20) hydrogen bonds : bond 0.05657 ( 846) hydrogen bonds : angle 3.97709 ( 2733) link_BETA1-4 : bond 0.00400 ( 5) link_BETA1-4 : angle 2.42439 ( 15) link_NAG-ASN : bond 0.00260 ( 10) link_NAG-ASN : angle 5.49697 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.671 Fit side-chains REVERT: A 321 ASP cc_start: 0.9177 (t0) cc_final: 0.8867 (t0) REVERT: A 342 PHE cc_start: 0.8934 (t80) cc_final: 0.7689 (m-10) REVERT: A 435 LYS cc_start: 0.8586 (mttt) cc_final: 0.7511 (mttm) REVERT: A 438 GLU cc_start: 0.8341 (pp20) cc_final: 0.7658 (pp20) REVERT: A 439 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8539 (mp0) REVERT: B 236 ASN cc_start: 0.8796 (m110) cc_final: 0.8529 (m-40) REVERT: B 283 MET cc_start: 0.9135 (mmm) cc_final: 0.8772 (mmp) REVERT: B 321 ASP cc_start: 0.9032 (t0) cc_final: 0.8595 (t0) REVERT: B 435 LYS cc_start: 0.8808 (mttt) cc_final: 0.8461 (mttp) REVERT: B 438 GLU cc_start: 0.8213 (pp20) cc_final: 0.7942 (pp20) REVERT: B 439 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8915 (mm-30) REVERT: B 454 GLU cc_start: 0.8627 (pt0) cc_final: 0.8357 (pp20) REVERT: B 476 SER cc_start: 0.9115 (t) cc_final: 0.8891 (p) REVERT: C 321 ASP cc_start: 0.9109 (t0) cc_final: 0.8569 (t0) REVERT: C 342 PHE cc_start: 0.8227 (t80) cc_final: 0.7350 (m-10) REVERT: C 435 LYS cc_start: 0.8706 (mttt) cc_final: 0.7861 (mttm) REVERT: C 438 GLU cc_start: 0.8148 (pp20) cc_final: 0.7247 (pp20) REVERT: C 439 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8351 (mp0) REVERT: C 476 SER cc_start: 0.9159 (t) cc_final: 0.8920 (p) REVERT: C 478 PHE cc_start: 0.8498 (t80) cc_final: 0.8243 (t80) REVERT: D 321 ASP cc_start: 0.9127 (t0) cc_final: 0.8760 (t0) REVERT: D 435 LYS cc_start: 0.8647 (mttt) cc_final: 0.8130 (mttm) REVERT: D 438 GLU cc_start: 0.8036 (pp20) cc_final: 0.7812 (pp20) REVERT: D 439 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8919 (mm-30) REVERT: D 454 GLU cc_start: 0.8666 (pt0) cc_final: 0.8385 (pp20) REVERT: E 275 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7559 (t80) REVERT: E 321 ASP cc_start: 0.9118 (t0) cc_final: 0.8699 (t0) REVERT: E 435 LYS cc_start: 0.8620 (mttt) cc_final: 0.8097 (mttm) REVERT: E 438 GLU cc_start: 0.8126 (pp20) cc_final: 0.7742 (pp20) REVERT: E 439 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8929 (mm-30) REVERT: E 454 GLU cc_start: 0.8603 (pt0) cc_final: 0.8307 (pp20) REVERT: E 476 SER cc_start: 0.9115 (t) cc_final: 0.8878 (p) outliers start: 29 outliers final: 13 residues processed: 239 average time/residue: 0.4692 time to fit residues: 127.9189 Evaluate side-chains 237 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 468 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 39 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 0.0570 chunk 98 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.062286 restraints weight = 75688.128| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.09 r_work: 0.2540 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16705 Z= 0.114 Angle : 0.595 11.197 22820 Z= 0.286 Chirality : 0.046 0.519 2605 Planarity : 0.004 0.033 2835 Dihedral : 5.873 33.049 2545 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.42 % Allowed : 19.89 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.13 (0.18), residues: 1985 helix: 2.87 (0.17), residues: 815 sheet: 0.66 (0.25), residues: 405 loop : 0.28 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 469 TYR 0.006 0.001 TYR C 232 PHE 0.007 0.001 PHE B 157 TRP 0.008 0.001 TRP E 82 HIS 0.002 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00247 (16680) covalent geometry : angle 0.55540 (22755) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.51393 ( 20) hydrogen bonds : bond 0.05032 ( 846) hydrogen bonds : angle 3.79614 ( 2733) link_BETA1-4 : bond 0.00106 ( 5) link_BETA1-4 : angle 2.54407 ( 15) link_NAG-ASN : bond 0.00457 ( 10) link_NAG-ASN : angle 5.51821 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.726 Fit side-chains REVERT: A 197 ASP cc_start: 0.8685 (t70) cc_final: 0.8216 (t0) REVERT: A 321 ASP cc_start: 0.9160 (t0) cc_final: 0.8852 (t0) REVERT: A 342 PHE cc_start: 0.8943 (t80) cc_final: 0.7687 (m-10) REVERT: A 435 LYS cc_start: 0.8523 (mttt) cc_final: 0.7296 (mttt) REVERT: A 438 GLU cc_start: 0.8213 (pp20) cc_final: 0.7564 (pp20) REVERT: A 439 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8404 (mp0) REVERT: B 197 ASP cc_start: 0.8641 (t70) cc_final: 0.8147 (t0) REVERT: B 257 ASP cc_start: 0.8980 (m-30) cc_final: 0.8716 (m-30) REVERT: B 283 MET cc_start: 0.9016 (mmm) cc_final: 0.8744 (mmp) REVERT: B 321 ASP cc_start: 0.9009 (t0) cc_final: 0.8562 (t0) REVERT: B 435 LYS cc_start: 0.8719 (mttt) cc_final: 0.8210 (mttp) REVERT: B 438 GLU cc_start: 0.8188 (pp20) cc_final: 0.7914 (pp20) REVERT: B 439 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8839 (mm-30) REVERT: B 454 GLU cc_start: 0.8512 (pt0) cc_final: 0.8271 (pp20) REVERT: B 476 SER cc_start: 0.9037 (t) cc_final: 0.8832 (p) REVERT: C 197 ASP cc_start: 0.8625 (t70) cc_final: 0.8151 (t0) REVERT: C 321 ASP cc_start: 0.9065 (t0) cc_final: 0.8526 (t0) REVERT: C 342 PHE cc_start: 0.8214 (t80) cc_final: 0.7319 (m-10) REVERT: C 435 LYS cc_start: 0.8626 (mttt) cc_final: 0.7708 (mttt) REVERT: C 438 GLU cc_start: 0.8136 (pp20) cc_final: 0.7323 (pp20) REVERT: C 439 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8340 (mp0) REVERT: C 476 SER cc_start: 0.9099 (t) cc_final: 0.8867 (p) REVERT: C 478 PHE cc_start: 0.8399 (t80) cc_final: 0.8161 (t80) REVERT: D 197 ASP cc_start: 0.8775 (t70) cc_final: 0.8303 (t0) REVERT: D 243 LEU cc_start: 0.8770 (mm) cc_final: 0.8458 (mt) REVERT: D 283 MET cc_start: 0.9049 (mmp) cc_final: 0.8746 (mmp) REVERT: D 321 ASP cc_start: 0.9083 (t0) cc_final: 0.8697 (t0) REVERT: D 435 LYS cc_start: 0.8624 (mttt) cc_final: 0.8183 (mttm) REVERT: D 438 GLU cc_start: 0.8020 (pp20) cc_final: 0.7790 (pp20) REVERT: D 439 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8859 (mm-30) REVERT: D 454 GLU cc_start: 0.8592 (pt0) cc_final: 0.8304 (pp20) REVERT: D 476 SER cc_start: 0.9047 (t) cc_final: 0.8764 (p) REVERT: E 197 ASP cc_start: 0.8658 (t70) cc_final: 0.8195 (t0) REVERT: E 275 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7497 (t80) REVERT: E 321 ASP cc_start: 0.9067 (t0) cc_final: 0.8632 (t0) REVERT: E 435 LYS cc_start: 0.8550 (mttt) cc_final: 0.7613 (mttp) REVERT: E 438 GLU cc_start: 0.8133 (pp20) cc_final: 0.7169 (pp20) REVERT: E 439 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8525 (mp0) REVERT: E 454 GLU cc_start: 0.8511 (pt0) cc_final: 0.8236 (pp20) REVERT: E 476 SER cc_start: 0.9055 (t) cc_final: 0.8825 (p) outliers start: 25 outliers final: 17 residues processed: 246 average time/residue: 0.4470 time to fit residues: 126.5150 Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.062483 restraints weight = 91815.339| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 4.47 r_work: 0.2567 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16705 Z= 0.138 Angle : 0.607 11.346 22820 Z= 0.291 Chirality : 0.046 0.524 2605 Planarity : 0.004 0.032 2835 Dihedral : 5.779 33.362 2545 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.42 % Allowed : 20.06 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.09 (0.18), residues: 1985 helix: 2.81 (0.17), residues: 820 sheet: 0.63 (0.25), residues: 405 loop : 0.27 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.007 0.001 TYR B 233 PHE 0.007 0.001 PHE C 157 TRP 0.006 0.001 TRP E 82 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00315 (16680) covalent geometry : angle 0.56943 (22755) SS BOND : bond 0.00762 ( 10) SS BOND : angle 1.45683 ( 20) hydrogen bonds : bond 0.05109 ( 846) hydrogen bonds : angle 3.81852 ( 2733) link_BETA1-4 : bond 0.00167 ( 5) link_BETA1-4 : angle 2.44751 ( 15) link_NAG-ASN : bond 0.00255 ( 10) link_NAG-ASN : angle 5.50036 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.667 Fit side-chains REVERT: A 197 ASP cc_start: 0.8746 (t70) cc_final: 0.8269 (t0) REVERT: A 321 ASP cc_start: 0.9185 (t0) cc_final: 0.8882 (t0) REVERT: A 342 PHE cc_start: 0.8927 (t80) cc_final: 0.7690 (m-10) REVERT: A 435 LYS cc_start: 0.8555 (mttt) cc_final: 0.7299 (mttt) REVERT: A 438 GLU cc_start: 0.8279 (pp20) cc_final: 0.7607 (pp20) REVERT: A 439 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8441 (mp0) REVERT: B 257 ASP cc_start: 0.8995 (m-30) cc_final: 0.8730 (m-30) REVERT: B 283 MET cc_start: 0.9029 (mmm) cc_final: 0.8762 (mmp) REVERT: B 321 ASP cc_start: 0.9037 (t0) cc_final: 0.8586 (t0) REVERT: B 435 LYS cc_start: 0.8764 (mttt) cc_final: 0.8410 (mttp) REVERT: B 438 GLU cc_start: 0.8193 (pp20) cc_final: 0.7935 (pp20) REVERT: B 439 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8955 (mm-30) REVERT: B 454 GLU cc_start: 0.8586 (pt0) cc_final: 0.8324 (pp20) REVERT: B 476 SER cc_start: 0.9114 (t) cc_final: 0.8891 (p) REVERT: C 197 ASP cc_start: 0.8685 (t70) cc_final: 0.8244 (t0) REVERT: C 321 ASP cc_start: 0.9110 (t0) cc_final: 0.8580 (t0) REVERT: C 342 PHE cc_start: 0.8298 (t80) cc_final: 0.7371 (m-10) REVERT: C 435 LYS cc_start: 0.8645 (mttt) cc_final: 0.7663 (mttt) REVERT: C 438 GLU cc_start: 0.8211 (pp20) cc_final: 0.7401 (pp20) REVERT: C 439 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8320 (mp0) REVERT: C 476 SER cc_start: 0.9176 (t) cc_final: 0.8934 (p) REVERT: C 478 PHE cc_start: 0.8465 (t80) cc_final: 0.8224 (t80) REVERT: D 197 ASP cc_start: 0.8828 (t70) cc_final: 0.8374 (t0) REVERT: D 243 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (mt) REVERT: D 283 MET cc_start: 0.9097 (mmp) cc_final: 0.8811 (mmp) REVERT: D 321 ASP cc_start: 0.9131 (t0) cc_final: 0.8755 (t0) REVERT: D 435 LYS cc_start: 0.8591 (mttt) cc_final: 0.8024 (mttm) REVERT: D 438 GLU cc_start: 0.8054 (pp20) cc_final: 0.7831 (pp20) REVERT: D 439 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8894 (mm-30) REVERT: D 454 GLU cc_start: 0.8654 (pt0) cc_final: 0.8343 (pp20) REVERT: D 476 SER cc_start: 0.9119 (t) cc_final: 0.8853 (p) REVERT: E 197 ASP cc_start: 0.8691 (t70) cc_final: 0.8228 (t0) REVERT: E 275 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7645 (t80) REVERT: E 321 ASP cc_start: 0.9124 (t0) cc_final: 0.8700 (t0) REVERT: E 435 LYS cc_start: 0.8607 (mttt) cc_final: 0.7982 (mttp) REVERT: E 438 GLU cc_start: 0.8150 (pp20) cc_final: 0.7667 (pp20) REVERT: E 439 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8787 (mm-30) REVERT: E 454 GLU cc_start: 0.8572 (pt0) cc_final: 0.8265 (pp20) REVERT: E 476 SER cc_start: 0.9114 (t) cc_final: 0.8888 (p) outliers start: 25 outliers final: 18 residues processed: 239 average time/residue: 0.4379 time to fit residues: 119.7207 Evaluate side-chains 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 0.0570 chunk 112 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.063065 restraints weight = 67735.613| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.87 r_work: 0.2589 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16705 Z= 0.137 Angle : 0.607 11.486 22820 Z= 0.291 Chirality : 0.046 0.531 2605 Planarity : 0.004 0.031 2835 Dihedral : 5.705 33.330 2545 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.25 % Allowed : 20.28 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.05 (0.18), residues: 1985 helix: 2.76 (0.17), residues: 820 sheet: 0.62 (0.25), residues: 405 loop : 0.29 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.007 0.001 TYR B 233 PHE 0.007 0.001 PHE C 157 TRP 0.007 0.001 TRP E 341 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00313 (16680) covalent geometry : angle 0.56783 (22755) SS BOND : bond 0.00756 ( 10) SS BOND : angle 1.47746 ( 20) hydrogen bonds : bond 0.05123 ( 846) hydrogen bonds : angle 3.82687 ( 2733) link_BETA1-4 : bond 0.00176 ( 5) link_BETA1-4 : angle 2.36364 ( 15) link_NAG-ASN : bond 0.00268 ( 10) link_NAG-ASN : angle 5.56810 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.606 Fit side-chains REVERT: A 321 ASP cc_start: 0.9174 (t0) cc_final: 0.8861 (t0) REVERT: A 342 PHE cc_start: 0.8918 (t80) cc_final: 0.7661 (m-10) REVERT: A 435 LYS cc_start: 0.8551 (mttt) cc_final: 0.7311 (mttt) REVERT: A 438 GLU cc_start: 0.8271 (pp20) cc_final: 0.7673 (pp20) REVERT: A 439 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8358 (mp0) REVERT: B 257 ASP cc_start: 0.8960 (m-30) cc_final: 0.8723 (m-30) REVERT: B 283 MET cc_start: 0.9023 (mmm) cc_final: 0.8760 (mmp) REVERT: B 321 ASP cc_start: 0.9024 (t0) cc_final: 0.8582 (t0) REVERT: B 435 LYS cc_start: 0.8741 (mttt) cc_final: 0.8209 (mttp) REVERT: B 438 GLU cc_start: 0.8186 (pp20) cc_final: 0.7898 (pp20) REVERT: B 439 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8868 (mm-30) REVERT: B 454 GLU cc_start: 0.8572 (pt0) cc_final: 0.8313 (pp20) REVERT: B 476 SER cc_start: 0.9111 (t) cc_final: 0.8886 (p) REVERT: C 197 ASP cc_start: 0.8648 (t70) cc_final: 0.8201 (t0) REVERT: C 321 ASP cc_start: 0.9095 (t0) cc_final: 0.8556 (t0) REVERT: C 342 PHE cc_start: 0.8332 (t80) cc_final: 0.7366 (m-10) REVERT: C 435 LYS cc_start: 0.8624 (mttt) cc_final: 0.7650 (mttt) REVERT: C 438 GLU cc_start: 0.8243 (pp20) cc_final: 0.7488 (pp20) REVERT: C 439 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8286 (mp0) REVERT: C 476 SER cc_start: 0.9181 (t) cc_final: 0.8933 (p) REVERT: C 478 PHE cc_start: 0.8445 (t80) cc_final: 0.8206 (t80) REVERT: D 197 ASP cc_start: 0.8780 (t70) cc_final: 0.8346 (t0) REVERT: D 243 LEU cc_start: 0.8820 (mm) cc_final: 0.8584 (mt) REVERT: D 283 MET cc_start: 0.9107 (mmp) cc_final: 0.8823 (mmp) REVERT: D 321 ASP cc_start: 0.9118 (t0) cc_final: 0.8740 (t0) REVERT: D 435 LYS cc_start: 0.8571 (mttt) cc_final: 0.8067 (mttm) REVERT: D 438 GLU cc_start: 0.8045 (pp20) cc_final: 0.7819 (pp20) REVERT: D 439 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8882 (mm-30) REVERT: D 454 GLU cc_start: 0.8672 (pt0) cc_final: 0.8382 (pp20) REVERT: D 476 SER cc_start: 0.9131 (t) cc_final: 0.8850 (p) REVERT: E 275 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7627 (t80) REVERT: E 321 ASP cc_start: 0.9114 (t0) cc_final: 0.8691 (t0) REVERT: E 435 LYS cc_start: 0.8577 (mttt) cc_final: 0.7944 (mttp) REVERT: E 438 GLU cc_start: 0.8136 (pp20) cc_final: 0.7679 (pp20) REVERT: E 439 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8771 (mm-30) REVERT: E 454 GLU cc_start: 0.8565 (pt0) cc_final: 0.8256 (pp20) REVERT: E 476 SER cc_start: 0.9114 (t) cc_final: 0.8886 (p) REVERT: E 478 PHE cc_start: 0.8510 (t80) cc_final: 0.8276 (t80) outliers start: 22 outliers final: 17 residues processed: 234 average time/residue: 0.4491 time to fit residues: 120.3821 Evaluate side-chains 240 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.063148 restraints weight = 81987.669| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.28 r_work: 0.2580 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16705 Z= 0.130 Angle : 0.607 11.368 22820 Z= 0.291 Chirality : 0.046 0.527 2605 Planarity : 0.004 0.031 2835 Dihedral : 5.660 33.170 2545 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.30 % Allowed : 20.23 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.07 (0.18), residues: 1985 helix: 2.76 (0.17), residues: 820 sheet: 0.63 (0.25), residues: 405 loop : 0.31 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.007 0.001 TYR B 233 PHE 0.007 0.001 PHE C 157 TRP 0.007 0.001 TRP B 341 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00295 (16680) covalent geometry : angle 0.56850 (22755) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.48068 ( 20) hydrogen bonds : bond 0.05014 ( 846) hydrogen bonds : angle 3.80616 ( 2733) link_BETA1-4 : bond 0.00131 ( 5) link_BETA1-4 : angle 2.33481 ( 15) link_NAG-ASN : bond 0.00301 ( 10) link_NAG-ASN : angle 5.52301 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.673 Fit side-chains REVERT: A 197 ASP cc_start: 0.8719 (t70) cc_final: 0.8255 (t0) REVERT: A 321 ASP cc_start: 0.9187 (t0) cc_final: 0.8874 (t0) REVERT: A 342 PHE cc_start: 0.8947 (t80) cc_final: 0.7691 (m-10) REVERT: A 435 LYS cc_start: 0.8585 (mttt) cc_final: 0.7354 (mttt) REVERT: A 438 GLU cc_start: 0.8247 (pp20) cc_final: 0.7653 (pp20) REVERT: A 439 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8364 (mp0) REVERT: B 257 ASP cc_start: 0.8957 (m-30) cc_final: 0.8708 (m-30) REVERT: B 283 MET cc_start: 0.8987 (mmm) cc_final: 0.8746 (mmp) REVERT: B 321 ASP cc_start: 0.9041 (t0) cc_final: 0.8601 (t0) REVERT: B 435 LYS cc_start: 0.8726 (mttt) cc_final: 0.8372 (mttp) REVERT: B 438 GLU cc_start: 0.8201 (pp20) cc_final: 0.7911 (pp20) REVERT: B 439 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8938 (mm-30) REVERT: B 454 GLU cc_start: 0.8553 (pt0) cc_final: 0.8293 (pp20) REVERT: B 476 SER cc_start: 0.9109 (t) cc_final: 0.8890 (p) REVERT: C 197 ASP cc_start: 0.8698 (t70) cc_final: 0.8231 (t0) REVERT: C 321 ASP cc_start: 0.9103 (t0) cc_final: 0.8566 (t0) REVERT: C 342 PHE cc_start: 0.8339 (t80) cc_final: 0.7339 (m-10) REVERT: C 435 LYS cc_start: 0.8664 (mttt) cc_final: 0.7691 (mttt) REVERT: C 438 GLU cc_start: 0.8250 (pp20) cc_final: 0.7521 (pp20) REVERT: C 439 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8308 (mp0) REVERT: C 476 SER cc_start: 0.9171 (t) cc_final: 0.8926 (p) REVERT: D 197 ASP cc_start: 0.8813 (t70) cc_final: 0.8367 (t0) REVERT: D 243 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8606 (mt) REVERT: D 283 MET cc_start: 0.9106 (mmp) cc_final: 0.8791 (mmp) REVERT: D 321 ASP cc_start: 0.9133 (t0) cc_final: 0.8758 (t0) REVERT: D 435 LYS cc_start: 0.8574 (mttt) cc_final: 0.7774 (mttm) REVERT: D 438 GLU cc_start: 0.8060 (pp20) cc_final: 0.7212 (pp20) REVERT: D 439 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8437 (mp0) REVERT: D 454 GLU cc_start: 0.8675 (pt0) cc_final: 0.8390 (pp20) REVERT: D 476 SER cc_start: 0.9123 (t) cc_final: 0.8841 (p) REVERT: E 197 ASP cc_start: 0.8675 (t70) cc_final: 0.8215 (t0) REVERT: E 275 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7562 (t80) REVERT: E 321 ASP cc_start: 0.9132 (t0) cc_final: 0.8712 (t0) REVERT: E 435 LYS cc_start: 0.8576 (mttt) cc_final: 0.7932 (mttp) REVERT: E 438 GLU cc_start: 0.8157 (pp20) cc_final: 0.7730 (pp20) REVERT: E 439 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8809 (mm-30) REVERT: E 454 GLU cc_start: 0.8569 (pt0) cc_final: 0.8261 (pp20) REVERT: E 476 SER cc_start: 0.9114 (t) cc_final: 0.8890 (p) REVERT: E 478 PHE cc_start: 0.8521 (t80) cc_final: 0.8295 (t80) outliers start: 23 outliers final: 17 residues processed: 239 average time/residue: 0.4514 time to fit residues: 124.2842 Evaluate side-chains 248 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.062570 restraints weight = 68822.089| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.93 r_work: 0.2550 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16705 Z= 0.122 Angle : 0.606 11.360 22820 Z= 0.289 Chirality : 0.046 0.523 2605 Planarity : 0.004 0.031 2835 Dihedral : 5.610 32.856 2545 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.47 % Allowed : 20.11 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.13 (0.18), residues: 1985 helix: 2.82 (0.17), residues: 825 sheet: 0.67 (0.25), residues: 405 loop : 0.31 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.006 0.001 TYR B 233 PHE 0.007 0.001 PHE C 157 TRP 0.007 0.001 TRP E 82 HIS 0.002 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00276 (16680) covalent geometry : angle 0.56763 (22755) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.48256 ( 20) hydrogen bonds : bond 0.04872 ( 846) hydrogen bonds : angle 3.76267 ( 2733) link_BETA1-4 : bond 0.00099 ( 5) link_BETA1-4 : angle 2.32793 ( 15) link_NAG-ASN : bond 0.00346 ( 10) link_NAG-ASN : angle 5.51124 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.11 seconds wall clock time: 94 minutes 15.94 seconds (5655.94 seconds total)