Starting phenix.real_space_refine on Wed Sep 17 22:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw6_60517/09_2025/8zw6_60517.map" } resolution = 2.75 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= 0.001 sd= 0.027 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 57 5.16 5 C 7341 2.51 5 N 2036 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11822 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3794 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 461} Chain breaks: 2 Chain: "B" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3818 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3805 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.44, per 1000 atoms: 0.29 Number of scatterers: 11822 At special positions: 0 Unit cell: (85, 88.4, 148.75, 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 57 16.00 O 2388 8.00 N 2036 7.00 C 7341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 479 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " BETA2-3 " GAL J 1 " - " SIA J 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL K 1 " - " SIA K 2 " " GAL L 1 " - " SIA L 2 " NAG-ASN " NAG A 601 " - " ASN A 40 " " NAG B 601 " - " ASN B 40 " " NAG C 601 " - " ASN C 40 " " NAG D 1 " - " ASN A 167 " " NAG E 1 " - " ASN A 287 " " NAG F 1 " - " ASN B 167 " " NAG G 1 " - " ASN B 287 " " NAG H 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 287 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 563.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 36 sheets defined 27.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.674A pdb=" N ASP A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.649A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.863A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.520A pdb=" N VAL A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 457 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.639A pdb=" N ASP B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL B 80 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 82 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.657A pdb=" N LEU B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.610A pdb=" N VAL B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 457 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 493 through 502 Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.641A pdb=" N ASP C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL C 80 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 81 " --> pdb=" O CYS C 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.547A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.591A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.595A pdb=" N ARG C 385 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 386 " --> pdb=" O LEU C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 386' Processing helix chain 'C' and resid 406 through 457 Processing helix chain 'C' and resid 476 through 486 Processing helix chain 'C' and resid 489 through 502 removed outlier: 4.520A pdb=" N TYR C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C 495 " --> pdb=" O ASP C 491 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 56 removed outlier: 5.872A pdb=" N ILE A 53 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS A 279 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 55 " --> pdb=" O CYS A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.014A pdb=" N PHE A 89 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.531A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 181 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 181 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.531A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 181 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AB1, first strand: chain 'A' and resid 138 through 143 removed outlier: 4.944A pdb=" N CYS A 141 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 146 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AB3, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.611A pdb=" N CYS A 307 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 391 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 363 through 368 removed outlier: 4.668A pdb=" N TYR B 353 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 470 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 462 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AB7, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'B' and resid 53 through 56 removed outlier: 5.892A pdb=" N ILE B 53 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N CYS B 279 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 55 " --> pdb=" O CYS B 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.003A pdb=" N PHE B 89 " --> pdb=" O MET B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.487A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE B 181 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.487A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 231 " --> pdb=" O HIS B 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AC4, first strand: chain 'B' and resid 138 through 143 removed outlier: 4.867A pdb=" N CYS B 141 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 146 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 166 through 171 Processing sheet with id=AC6, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.689A pdb=" N CYS B 307 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B 391 " --> pdb=" O CYS B 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 364 through 365 removed outlier: 3.681A pdb=" N HIS C 357 " --> pdb=" O GLY C 364 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AD1, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'C' and resid 53 through 56 removed outlier: 5.583A pdb=" N ILE C 53 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N CYS C 279 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 55 " --> pdb=" O CYS C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.817A pdb=" N LEU C 61 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE C 89 " --> pdb=" O MET C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.537A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE C 181 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.537A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AD7, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.906A pdb=" N CYS C 141 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 146 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AD9, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.742A pdb=" N CYS C 307 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN C 391 " --> pdb=" O CYS C 307 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1305 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: 2.23 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3909 1.34 - 1.46: 2852 1.46 - 1.58: 5218 1.58 - 1.70: 3 1.70 - 1.82: 78 Bond restraints: 12060 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 12055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 15976 1.54 - 3.09: 295 3.09 - 4.63: 54 4.63 - 6.17: 17 6.17 - 7.71: 9 Bond angle restraints: 16351 Sorted by residual: angle pdb=" C ARG C 64 " pdb=" CA ARG C 64 " pdb=" CB ARG C 64 " ideal model delta sigma weight residual 117.23 110.79 6.44 1.36e+00 5.41e-01 2.24e+01 angle pdb=" N ILE B 349 " pdb=" CA ILE B 349 " pdb=" C ILE B 349 " ideal model delta sigma weight residual 113.20 109.57 3.63 9.60e-01 1.09e+00 1.43e+01 angle pdb=" CA ARG C 64 " pdb=" C ARG C 64 " pdb=" N ASP C 65 " ideal model delta sigma weight residual 119.98 117.19 2.79 8.50e-01 1.38e+00 1.08e+01 angle pdb=" N ILE C 349 " pdb=" CA ILE C 349 " pdb=" C ILE C 349 " ideal model delta sigma weight residual 113.20 110.35 2.85 9.60e-01 1.09e+00 8.82e+00 angle pdb=" CA LEU A 113 " pdb=" CB LEU A 113 " pdb=" CG LEU A 113 " ideal model delta sigma weight residual 116.30 124.01 -7.71 3.50e+00 8.16e-02 4.86e+00 ... (remaining 16346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 7118 22.09 - 44.18: 450 44.18 - 66.27: 53 66.27 - 88.36: 37 88.36 - 110.44: 17 Dihedral angle restraints: 7675 sinusoidal: 3504 harmonic: 4171 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.27 110.44 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.92 109.79 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.77 108.94 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 7672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1627 0.063 - 0.127: 232 0.127 - 0.190: 11 0.190 - 0.254: 0 0.254 - 0.317: 6 Chirality restraints: 1876 Sorted by residual: chirality pdb=" C2 SIA L 2 " pdb=" O3 GAL L 1 " pdb=" C1 SIA L 2 " pdb=" O6 SIA L 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.51e+02 chirality pdb=" C2 SIA J 2 " pdb=" O3 GAL J 1 " pdb=" C1 SIA J 2 " pdb=" O6 SIA J 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.50e+02 chirality pdb=" C2 SIA K 2 " pdb=" O3 GAL K 1 " pdb=" C1 SIA K 2 " pdb=" O6 SIA K 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.50e+02 ... (remaining 1873 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 23 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 75 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 76 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 75 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 76 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.019 5.00e-02 4.00e+02 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 344 2.71 - 3.26: 10481 3.26 - 3.81: 18589 3.81 - 4.35: 24196 4.35 - 4.90: 41368 Nonbonded interactions: 94978 Sorted by model distance: nonbonded pdb=" OE2 GLU A 192 " pdb=" O9 SIA K 2 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR C 285 " pdb=" O GLY C 288 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU B 462 " pdb=" OH TYR B 472 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU B 192 " pdb=" O9 SIA J 2 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU C 192 " pdb=" O9 SIA L 2 " model vdw 2.270 3.040 ... (remaining 94973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 462 or (resid 463 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 464 through 601) \ ) selection = (chain 'B' and (resid 12 through 99 or resid 101 through 125 or (resid 126 and ( \ name N or name CA or name C or name O or name CB )) or resid 127 through 327 or \ resid 337 through 601)) selection = (chain 'C' and (resid 12 through 99 or resid 101 through 462 or (resid 463 and ( \ name N or name CA or name C or name O or name CB or name CG )) or resid 464 thro \ ugh 601)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.003 0.066 12105 Z= 0.161 Angle : 0.626 11.794 16468 Z= 0.284 Chirality : 0.046 0.317 1876 Planarity : 0.004 0.049 2100 Dihedral : 15.479 110.444 4937 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.79 (0.21), residues: 1433 helix: 3.50 (0.25), residues: 334 sheet: 0.68 (0.30), residues: 300 loop : -0.91 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.018 0.001 TYR C 493 PHE 0.007 0.001 PHE B 127 TRP 0.010 0.001 TRP B 423 HIS 0.007 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00315 (12060) covalent geometry : angle 0.56741 (16351) SS BOND : bond 0.00185 ( 18) SS BOND : angle 1.02382 ( 36) hydrogen bonds : bond 0.16786 ( 461) hydrogen bonds : angle 6.45713 ( 1305) link_ALPHA1-3 : bond 0.00411 ( 3) link_ALPHA1-3 : angle 1.56860 ( 9) link_ALPHA1-6 : bond 0.00360 ( 3) link_ALPHA1-6 : angle 1.54083 ( 9) link_BETA1-4 : bond 0.00301 ( 9) link_BETA1-4 : angle 1.73906 ( 27) link_BETA2-3 : bond 0.06573 ( 3) link_BETA2-3 : angle 10.48171 ( 9) link_NAG-ASN : bond 0.00151 ( 9) link_NAG-ASN : angle 1.17331 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.6884 (t0) cc_final: 0.6651 (t0) REVERT: A 322 MET cc_start: 0.8706 (ptp) cc_final: 0.8460 (ptm) REVERT: A 470 LYS cc_start: 0.8018 (tttt) cc_final: 0.7656 (tptp) REVERT: A 489 ASP cc_start: 0.7369 (t0) cc_final: 0.7149 (t0) REVERT: A 491 ASP cc_start: 0.7896 (m-30) cc_final: 0.7645 (m-30) REVERT: B 459 GLU cc_start: 0.6934 (tp30) cc_final: 0.6375 (tp30) REVERT: B 464 MET cc_start: 0.7941 (mtm) cc_final: 0.7659 (mtm) REVERT: B 485 ASN cc_start: 0.7804 (m-40) cc_final: 0.7526 (m-40) REVERT: B 491 ASP cc_start: 0.7652 (m-30) cc_final: 0.7438 (m-30) REVERT: B 501 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7582 (mtm180) REVERT: C 161 SER cc_start: 0.8531 (p) cc_final: 0.8293 (t) REVERT: C 211 SER cc_start: 0.8173 (p) cc_final: 0.7947 (m) REVERT: C 451 GLU cc_start: 0.7230 (tp30) cc_final: 0.6971 (tp30) REVERT: C 481 GLU cc_start: 0.7261 (tt0) cc_final: 0.6714 (tm-30) REVERT: C 485 ASN cc_start: 0.7572 (m-40) cc_final: 0.7325 (m110) outliers start: 0 outliers final: 1 residues processed: 257 average time/residue: 0.6833 time to fit residues: 188.5091 Evaluate side-chains 215 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN B 195 ASN B 343 ASN B 384 ASN C 24 ASN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088618 restraints weight = 17583.259| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.79 r_work: 0.3011 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12105 Z= 0.140 Angle : 0.516 8.581 16468 Z= 0.266 Chirality : 0.043 0.183 1876 Planarity : 0.004 0.037 2100 Dihedral : 10.819 85.173 2212 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.13 % Allowed : 7.81 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.85 (0.21), residues: 1433 helix: 3.56 (0.25), residues: 334 sheet: 0.84 (0.29), residues: 305 loop : -0.94 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 222 TYR 0.016 0.001 TYR B 493 PHE 0.015 0.001 PHE B 355 TRP 0.007 0.001 TRP C 236 HIS 0.007 0.002 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (12060) covalent geometry : angle 0.49933 (16351) SS BOND : bond 0.00261 ( 18) SS BOND : angle 1.04983 ( 36) hydrogen bonds : bond 0.06150 ( 461) hydrogen bonds : angle 4.79342 ( 1305) link_ALPHA1-3 : bond 0.00799 ( 3) link_ALPHA1-3 : angle 2.33158 ( 9) link_ALPHA1-6 : bond 0.00454 ( 3) link_ALPHA1-6 : angle 1.81855 ( 9) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.86553 ( 27) link_BETA2-3 : bond 0.00809 ( 3) link_BETA2-3 : angle 2.74467 ( 9) link_NAG-ASN : bond 0.00187 ( 9) link_NAG-ASN : angle 1.10965 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7829 (t0) cc_final: 0.7480 (t0) REVERT: A 301 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8363 (ptpp) REVERT: A 322 MET cc_start: 0.8987 (ptp) cc_final: 0.8781 (ptm) REVERT: A 489 ASP cc_start: 0.7797 (t0) cc_final: 0.7584 (t70) REVERT: A 498 LEU cc_start: 0.8344 (mm) cc_final: 0.8096 (mt) REVERT: B 33 ASP cc_start: 0.7925 (m-30) cc_final: 0.7706 (t0) REVERT: B 106 ASP cc_start: 0.7646 (t0) cc_final: 0.7327 (t0) REVERT: B 446 MET cc_start: 0.8823 (tpt) cc_final: 0.8434 (tpt) REVERT: B 459 GLU cc_start: 0.7500 (tp30) cc_final: 0.7012 (tp30) REVERT: B 491 ASP cc_start: 0.7986 (m-30) cc_final: 0.7774 (m-30) REVERT: B 501 ARG cc_start: 0.8562 (mtp180) cc_final: 0.8002 (mtm180) REVERT: C 161 SER cc_start: 0.9057 (p) cc_final: 0.8767 (t) REVERT: C 211 SER cc_start: 0.8384 (p) cc_final: 0.8131 (m) REVERT: C 212 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: C 266 ARG cc_start: 0.7803 (ptt90) cc_final: 0.7540 (ptt90) REVERT: C 342 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 451 GLU cc_start: 0.8029 (tp30) cc_final: 0.7707 (tp30) REVERT: C 459 GLU cc_start: 0.7511 (tp30) cc_final: 0.7250 (tp30) outliers start: 27 outliers final: 14 residues processed: 242 average time/residue: 0.6226 time to fit residues: 162.7319 Evaluate side-chains 234 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN B 195 ASN B 343 ASN B 384 ASN C 485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087783 restraints weight = 17578.180| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.79 r_work: 0.2995 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.004 0.029 12105 Z= 0.172 Angle : 0.528 8.224 16468 Z= 0.272 Chirality : 0.044 0.203 1876 Planarity : 0.004 0.041 2100 Dihedral : 10.351 81.944 2212 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.58 % Allowed : 11.13 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.77 (0.21), residues: 1433 helix: 3.43 (0.25), residues: 334 sheet: 0.88 (0.30), residues: 308 loop : -1.01 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 152 TYR 0.017 0.002 TYR B 107 PHE 0.014 0.002 PHE B 127 TRP 0.008 0.001 TRP C 236 HIS 0.008 0.002 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00415 (12060) covalent geometry : angle 0.51085 (16351) SS BOND : bond 0.00305 ( 18) SS BOND : angle 1.01235 ( 36) hydrogen bonds : bond 0.06486 ( 461) hydrogen bonds : angle 4.57024 ( 1305) link_ALPHA1-3 : bond 0.00837 ( 3) link_ALPHA1-3 : angle 1.85685 ( 9) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.80072 ( 9) link_BETA1-4 : bond 0.00347 ( 9) link_BETA1-4 : angle 1.75402 ( 27) link_BETA2-3 : bond 0.00267 ( 3) link_BETA2-3 : angle 3.37752 ( 9) link_NAG-ASN : bond 0.00111 ( 9) link_NAG-ASN : angle 1.23878 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7827 (t0) cc_final: 0.7493 (t0) REVERT: A 485 ASN cc_start: 0.8022 (m-40) cc_final: 0.7751 (m-40) REVERT: A 498 LEU cc_start: 0.8375 (mm) cc_final: 0.8144 (mt) REVERT: B 33 ASP cc_start: 0.7933 (m-30) cc_final: 0.7721 (t0) REVERT: B 348 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8138 (ttm) REVERT: B 477 ASN cc_start: 0.8319 (m110) cc_final: 0.7961 (m-40) REVERT: B 491 ASP cc_start: 0.8040 (m-30) cc_final: 0.7816 (m-30) REVERT: B 501 ARG cc_start: 0.8595 (mtp180) cc_final: 0.8295 (mtp180) REVERT: C 66 CYS cc_start: 0.7438 (m) cc_final: 0.7129 (m) REVERT: C 161 SER cc_start: 0.9029 (p) cc_final: 0.8760 (t) REVERT: C 211 SER cc_start: 0.8410 (p) cc_final: 0.8167 (m) REVERT: C 229 SER cc_start: 0.8774 (p) cc_final: 0.8491 (t) REVERT: C 266 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7551 (ptt90) REVERT: C 342 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 451 GLU cc_start: 0.8079 (tp30) cc_final: 0.7732 (tp30) outliers start: 20 outliers final: 10 residues processed: 237 average time/residue: 0.6639 time to fit residues: 169.2468 Evaluate side-chains 239 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 384 ASN B 35 GLN B 195 ASN B 343 ASN C 24 ASN C 485 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086491 restraints weight = 17510.455| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.77 r_work: 0.2970 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12105 Z= 0.237 Angle : 0.582 9.533 16468 Z= 0.299 Chirality : 0.046 0.238 1876 Planarity : 0.004 0.045 2100 Dihedral : 10.039 79.235 2210 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.84 % Allowed : 10.66 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.59 (0.21), residues: 1433 helix: 3.16 (0.25), residues: 334 sheet: 1.00 (0.31), residues: 291 loop : -1.12 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 263 TYR 0.025 0.002 TYR B 107 PHE 0.020 0.002 PHE B 127 TRP 0.012 0.001 TRP C 236 HIS 0.011 0.002 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00585 (12060) covalent geometry : angle 0.56446 (16351) SS BOND : bond 0.00547 ( 18) SS BOND : angle 1.28994 ( 36) hydrogen bonds : bond 0.07184 ( 461) hydrogen bonds : angle 4.59601 ( 1305) link_ALPHA1-3 : bond 0.00810 ( 3) link_ALPHA1-3 : angle 1.87649 ( 9) link_ALPHA1-6 : bond 0.00524 ( 3) link_ALPHA1-6 : angle 1.51038 ( 9) link_BETA1-4 : bond 0.00333 ( 9) link_BETA1-4 : angle 1.89540 ( 27) link_BETA2-3 : bond 0.00128 ( 3) link_BETA2-3 : angle 3.40067 ( 9) link_NAG-ASN : bond 0.00195 ( 9) link_NAG-ASN : angle 1.49929 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 298 ASN cc_start: 0.8448 (t0) cc_final: 0.7974 (t0) REVERT: A 403 GLU cc_start: 0.7317 (tp30) cc_final: 0.6919 (tp30) REVERT: A 498 LEU cc_start: 0.8424 (mm) cc_final: 0.8209 (mt) REVERT: B 33 ASP cc_start: 0.7938 (m-30) cc_final: 0.7736 (t0) REVERT: B 348 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8183 (ttm) REVERT: B 398 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 491 ASP cc_start: 0.8109 (m-30) cc_final: 0.7870 (m-30) REVERT: C 161 SER cc_start: 0.9008 (p) cc_final: 0.8755 (t) REVERT: C 207 SER cc_start: 0.8614 (p) cc_final: 0.8332 (m) REVERT: C 211 SER cc_start: 0.8463 (p) cc_final: 0.8219 (m) REVERT: C 212 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8590 (pt0) REVERT: C 229 SER cc_start: 0.8747 (p) cc_final: 0.8511 (t) REVERT: C 266 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7585 (ptt90) REVERT: C 323 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: C 342 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7759 (mm-30) REVERT: C 451 GLU cc_start: 0.8171 (tp30) cc_final: 0.7929 (mm-30) REVERT: C 458 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7654 (ttp-170) outliers start: 36 outliers final: 17 residues processed: 258 average time/residue: 0.6460 time to fit residues: 179.7031 Evaluate side-chains 262 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 24 ASN C 485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088467 restraints weight = 17303.778| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.78 r_work: 0.3005 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12105 Z= 0.110 Angle : 0.488 7.966 16468 Z= 0.251 Chirality : 0.042 0.211 1876 Planarity : 0.004 0.039 2100 Dihedral : 9.365 72.428 2210 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.50 % Allowed : 13.10 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.79 (0.21), residues: 1433 helix: 3.52 (0.25), residues: 335 sheet: 0.88 (0.30), residues: 310 loop : -1.04 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 454 TYR 0.018 0.001 TYR B 107 PHE 0.010 0.001 PHE B 355 TRP 0.008 0.001 TRP C 236 HIS 0.008 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00243 (12060) covalent geometry : angle 0.47219 (16351) SS BOND : bond 0.00214 ( 18) SS BOND : angle 1.09590 ( 36) hydrogen bonds : bond 0.06106 ( 461) hydrogen bonds : angle 4.36602 ( 1305) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 1.81585 ( 9) link_ALPHA1-6 : bond 0.00833 ( 3) link_ALPHA1-6 : angle 1.67724 ( 9) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.55823 ( 27) link_BETA2-3 : bond 0.00091 ( 3) link_BETA2-3 : angle 2.80314 ( 9) link_NAG-ASN : bond 0.00178 ( 9) link_NAG-ASN : angle 1.14309 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: A 203 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8266 (ttp80) REVERT: A 298 ASN cc_start: 0.8310 (t0) cc_final: 0.7924 (t0) REVERT: A 403 GLU cc_start: 0.7316 (tp30) cc_final: 0.7011 (tp30) REVERT: A 485 ASN cc_start: 0.8139 (m-40) cc_final: 0.7849 (m-40) REVERT: B 33 ASP cc_start: 0.7976 (m-30) cc_final: 0.7769 (t0) REVERT: B 64 ARG cc_start: 0.8175 (mtm180) cc_final: 0.7969 (mtm-85) REVERT: B 398 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 458 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7579 (mtm-85) REVERT: B 491 ASP cc_start: 0.8073 (m-30) cc_final: 0.7842 (m-30) REVERT: C 161 SER cc_start: 0.8993 (p) cc_final: 0.8722 (t) REVERT: C 207 SER cc_start: 0.8561 (p) cc_final: 0.8331 (m) REVERT: C 211 SER cc_start: 0.8467 (p) cc_final: 0.8215 (m) REVERT: C 212 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: C 229 SER cc_start: 0.8693 (p) cc_final: 0.8480 (t) REVERT: C 266 ARG cc_start: 0.7825 (ptt90) cc_final: 0.7539 (ptt90) REVERT: C 277 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7106 (mm-30) REVERT: C 323 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7606 (mtp85) REVERT: C 342 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7540 (mm-30) REVERT: C 357 HIS cc_start: 0.8490 (p90) cc_final: 0.8205 (p-80) REVERT: C 451 GLU cc_start: 0.8141 (tp30) cc_final: 0.7893 (mm-30) outliers start: 19 outliers final: 13 residues processed: 250 average time/residue: 0.6658 time to fit residues: 179.2550 Evaluate side-chains 256 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN B 195 ASN B 343 ASN B 409 GLN C 485 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086106 restraints weight = 17439.059| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.78 r_work: 0.2981 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12105 Z= 0.259 Angle : 0.593 10.570 16468 Z= 0.302 Chirality : 0.046 0.264 1876 Planarity : 0.004 0.043 2100 Dihedral : 9.445 72.165 2210 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.68 % Allowed : 12.00 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.60 (0.21), residues: 1433 helix: 3.28 (0.25), residues: 333 sheet: 0.88 (0.30), residues: 301 loop : -1.15 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.025 0.002 TYR B 107 PHE 0.019 0.002 PHE B 127 TRP 0.012 0.001 TRP C 236 HIS 0.011 0.002 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00641 (12060) covalent geometry : angle 0.57487 (16351) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.39606 ( 36) hydrogen bonds : bond 0.07200 ( 461) hydrogen bonds : angle 4.47654 ( 1305) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 1.86661 ( 9) link_ALPHA1-6 : bond 0.00702 ( 3) link_ALPHA1-6 : angle 1.34214 ( 9) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 1.91524 ( 27) link_BETA2-3 : bond 0.00066 ( 3) link_BETA2-3 : angle 3.43307 ( 9) link_NAG-ASN : bond 0.00227 ( 9) link_NAG-ASN : angle 1.46797 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (ttm) REVERT: A 191 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: A 301 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8426 (ptpp) REVERT: A 403 GLU cc_start: 0.7348 (tp30) cc_final: 0.7062 (tp30) REVERT: B 64 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7907 (mtt180) REVERT: B 348 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8157 (ttm) REVERT: B 398 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 442 THR cc_start: 0.8531 (m) cc_final: 0.8330 (m) REVERT: B 458 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (mtm-85) REVERT: C 52 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: C 161 SER cc_start: 0.8988 (p) cc_final: 0.8721 (t) REVERT: C 207 SER cc_start: 0.8578 (p) cc_final: 0.8348 (m) REVERT: C 211 SER cc_start: 0.8481 (p) cc_final: 0.8221 (m) REVERT: C 212 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: C 229 SER cc_start: 0.8738 (p) cc_final: 0.8514 (t) REVERT: C 266 ARG cc_start: 0.7884 (ptt90) cc_final: 0.7655 (ptt90) REVERT: C 277 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7104 (mm-30) REVERT: C 323 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7605 (mtp85) REVERT: C 451 GLU cc_start: 0.8182 (tp30) cc_final: 0.7936 (mm-30) REVERT: C 458 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7631 (ttp-170) outliers start: 34 outliers final: 16 residues processed: 258 average time/residue: 0.6732 time to fit residues: 186.7850 Evaluate side-chains 265 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 143 optimal weight: 0.0070 chunk 142 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 24 ASN C 485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087888 restraints weight = 17361.256| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.78 r_work: 0.3006 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12105 Z= 0.136 Angle : 0.507 8.584 16468 Z= 0.261 Chirality : 0.043 0.235 1876 Planarity : 0.004 0.040 2100 Dihedral : 8.925 70.292 2210 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.89 % Allowed : 13.65 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.73 (0.21), residues: 1433 helix: 3.54 (0.25), residues: 334 sheet: 0.82 (0.30), residues: 310 loop : -1.10 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 454 TYR 0.017 0.001 TYR B 107 PHE 0.012 0.001 PHE B 355 TRP 0.009 0.001 TRP C 236 HIS 0.013 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00318 (12060) covalent geometry : angle 0.49123 (16351) SS BOND : bond 0.00232 ( 18) SS BOND : angle 1.29555 ( 36) hydrogen bonds : bond 0.06360 ( 461) hydrogen bonds : angle 4.33010 ( 1305) link_ALPHA1-3 : bond 0.00964 ( 3) link_ALPHA1-3 : angle 1.81152 ( 9) link_ALPHA1-6 : bond 0.00894 ( 3) link_ALPHA1-6 : angle 1.47588 ( 9) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.59015 ( 27) link_BETA2-3 : bond 0.00060 ( 3) link_BETA2-3 : angle 2.87254 ( 9) link_NAG-ASN : bond 0.00159 ( 9) link_NAG-ASN : angle 1.24805 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8559 (ttm) cc_final: 0.8327 (ttm) REVERT: A 191 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: A 203 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8272 (ttp80) REVERT: A 298 ASN cc_start: 0.8399 (t0) cc_final: 0.8101 (t0) REVERT: A 301 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8425 (ptpp) REVERT: A 403 GLU cc_start: 0.7328 (tp30) cc_final: 0.7014 (tp30) REVERT: A 485 ASN cc_start: 0.8164 (m-40) cc_final: 0.7873 (m-40) REVERT: B 346 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 398 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 442 THR cc_start: 0.8494 (m) cc_final: 0.8259 (m) REVERT: B 458 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7709 (mtm-85) REVERT: C 24 ASN cc_start: 0.8367 (p0) cc_final: 0.8134 (p0) REVERT: C 103 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7960 (p0) REVERT: C 161 SER cc_start: 0.8963 (p) cc_final: 0.8685 (t) REVERT: C 211 SER cc_start: 0.8461 (p) cc_final: 0.8214 (m) REVERT: C 212 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: C 229 SER cc_start: 0.8690 (p) cc_final: 0.8488 (t) REVERT: C 266 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7604 (ptt90) REVERT: C 277 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7126 (mm-30) REVERT: C 323 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7632 (mtp85) REVERT: C 451 GLU cc_start: 0.8154 (tp30) cc_final: 0.7912 (mm-30) REVERT: C 458 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7448 (ttp-170) outliers start: 24 outliers final: 12 residues processed: 260 average time/residue: 0.6754 time to fit residues: 188.6604 Evaluate side-chains 264 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 485 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086343 restraints weight = 17399.799| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.78 r_work: 0.2986 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12105 Z= 0.223 Angle : 0.579 10.182 16468 Z= 0.295 Chirality : 0.045 0.265 1876 Planarity : 0.004 0.042 2100 Dihedral : 8.839 70.595 2210 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.89 % Allowed : 14.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.60 (0.21), residues: 1433 helix: 3.35 (0.25), residues: 334 sheet: 0.77 (0.30), residues: 310 loop : -1.16 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.020 0.002 TYR B 107 PHE 0.020 0.002 PHE B 127 TRP 0.012 0.001 TRP C 236 HIS 0.013 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00548 (12060) covalent geometry : angle 0.56133 (16351) SS BOND : bond 0.00374 ( 18) SS BOND : angle 1.43812 ( 36) hydrogen bonds : bond 0.06994 ( 461) hydrogen bonds : angle 4.39982 ( 1305) link_ALPHA1-3 : bond 0.00895 ( 3) link_ALPHA1-3 : angle 1.83635 ( 9) link_ALPHA1-6 : bond 0.00843 ( 3) link_ALPHA1-6 : angle 1.39256 ( 9) link_BETA1-4 : bond 0.00379 ( 9) link_BETA1-4 : angle 1.81592 ( 27) link_BETA2-3 : bond 0.00072 ( 3) link_BETA2-3 : angle 3.27072 ( 9) link_NAG-ASN : bond 0.00209 ( 9) link_NAG-ASN : angle 1.43394 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8362 (ttm) REVERT: A 191 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: A 203 ARG cc_start: 0.8742 (ttm170) cc_final: 0.8294 (ttp80) REVERT: A 298 ASN cc_start: 0.8463 (t0) cc_final: 0.8194 (t0) REVERT: A 301 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8411 (ptpp) REVERT: A 403 GLU cc_start: 0.7378 (tp30) cc_final: 0.7099 (tp30) REVERT: A 485 ASN cc_start: 0.8192 (m-40) cc_final: 0.7902 (m-40) REVERT: B 346 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 348 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8176 (ttm) REVERT: B 398 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 458 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7914 (mtm-85) REVERT: C 24 ASN cc_start: 0.8415 (p0) cc_final: 0.8168 (p0) REVERT: C 103 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (p0) REVERT: C 161 SER cc_start: 0.8953 (p) cc_final: 0.8661 (t) REVERT: C 211 SER cc_start: 0.8462 (p) cc_final: 0.8216 (m) REVERT: C 212 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: C 229 SER cc_start: 0.8713 (p) cc_final: 0.8500 (t) REVERT: C 266 ARG cc_start: 0.7878 (ptt90) cc_final: 0.7636 (ptt90) REVERT: C 277 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 323 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: C 451 GLU cc_start: 0.8200 (tp30) cc_final: 0.7956 (mm-30) REVERT: C 458 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7586 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 255 average time/residue: 0.6722 time to fit residues: 184.2059 Evaluate side-chains 262 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 380 ASN C 485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087587 restraints weight = 17167.053| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.76 r_work: 0.3003 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12105 Z= 0.151 Angle : 0.524 9.453 16468 Z= 0.269 Chirality : 0.043 0.244 1876 Planarity : 0.004 0.040 2100 Dihedral : 8.477 70.772 2210 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.05 % Allowed : 14.52 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.70 (0.21), residues: 1433 helix: 3.50 (0.25), residues: 334 sheet: 0.80 (0.30), residues: 310 loop : -1.11 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 454 TYR 0.018 0.001 TYR B 107 PHE 0.012 0.001 PHE A 127 TRP 0.010 0.001 TRP C 236 HIS 0.012 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00359 (12060) covalent geometry : angle 0.50747 (16351) SS BOND : bond 0.00317 ( 18) SS BOND : angle 1.40495 ( 36) hydrogen bonds : bond 0.06488 ( 461) hydrogen bonds : angle 4.31513 ( 1305) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.78431 ( 9) link_ALPHA1-6 : bond 0.00985 ( 3) link_ALPHA1-6 : angle 1.43682 ( 9) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.62011 ( 27) link_BETA2-3 : bond 0.00065 ( 3) link_BETA2-3 : angle 2.89940 ( 9) link_NAG-ASN : bond 0.00163 ( 9) link_NAG-ASN : angle 1.30120 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8336 (ttm) REVERT: A 191 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: A 203 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8277 (ttp80) REVERT: A 298 ASN cc_start: 0.8412 (t0) cc_final: 0.8128 (t0) REVERT: A 301 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8424 (ptpp) REVERT: A 403 GLU cc_start: 0.7355 (tp30) cc_final: 0.7090 (tp30) REVERT: A 485 ASN cc_start: 0.8167 (m-40) cc_final: 0.7873 (m-40) REVERT: B 314 ASN cc_start: 0.8155 (p0) cc_final: 0.7546 (t0) REVERT: B 348 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8083 (ttm) REVERT: B 398 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 458 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7779 (mtm-85) REVERT: C 24 ASN cc_start: 0.8366 (p0) cc_final: 0.8114 (p0) REVERT: C 103 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7899 (p0) REVERT: C 161 SER cc_start: 0.8932 (p) cc_final: 0.8634 (t) REVERT: C 211 SER cc_start: 0.8465 (p) cc_final: 0.8222 (m) REVERT: C 212 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: C 229 SER cc_start: 0.8680 (p) cc_final: 0.8480 (t) REVERT: C 266 ARG cc_start: 0.7869 (ptt90) cc_final: 0.7634 (ptt90) REVERT: C 277 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 323 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7633 (mtp85) REVERT: C 451 GLU cc_start: 0.8182 (tp30) cc_final: 0.7935 (mm-30) REVERT: C 458 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7424 (ttp-170) outliers start: 26 outliers final: 15 residues processed: 250 average time/residue: 0.6850 time to fit residues: 183.9497 Evaluate side-chains 264 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 485 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087720 restraints weight = 17330.146| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.77 r_work: 0.3005 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12105 Z= 0.154 Angle : 0.531 9.709 16468 Z= 0.272 Chirality : 0.043 0.241 1876 Planarity : 0.004 0.040 2100 Dihedral : 8.274 70.611 2210 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.97 % Allowed : 14.68 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.71 (0.21), residues: 1433 helix: 3.51 (0.25), residues: 335 sheet: 0.80 (0.30), residues: 310 loop : -1.11 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 454 TYR 0.018 0.001 TYR B 493 PHE 0.013 0.001 PHE A 127 TRP 0.010 0.001 TRP C 236 HIS 0.012 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00369 (12060) covalent geometry : angle 0.51502 (16351) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.42023 ( 36) hydrogen bonds : bond 0.06472 ( 461) hydrogen bonds : angle 4.28942 ( 1305) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 1.79223 ( 9) link_ALPHA1-6 : bond 0.01011 ( 3) link_ALPHA1-6 : angle 1.40155 ( 9) link_BETA1-4 : bond 0.00419 ( 9) link_BETA1-4 : angle 1.64932 ( 27) link_BETA2-3 : bond 0.00047 ( 3) link_BETA2-3 : angle 2.91701 ( 9) link_NAG-ASN : bond 0.00181 ( 9) link_NAG-ASN : angle 1.29195 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (ttm) REVERT: A 191 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 203 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8270 (ttp80) REVERT: A 298 ASN cc_start: 0.8417 (t0) cc_final: 0.8138 (t0) REVERT: A 301 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: A 403 GLU cc_start: 0.7354 (tp30) cc_final: 0.7088 (tp30) REVERT: A 485 ASN cc_start: 0.8167 (m-40) cc_final: 0.7873 (m-40) REVERT: B 314 ASN cc_start: 0.8166 (p0) cc_final: 0.7569 (t0) REVERT: B 348 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8080 (ttm) REVERT: B 398 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8024 (mm-30) REVERT: B 458 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7753 (mtm-85) REVERT: C 24 ASN cc_start: 0.8364 (p0) cc_final: 0.8112 (p0) REVERT: C 103 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7888 (p0) REVERT: C 161 SER cc_start: 0.8937 (p) cc_final: 0.8634 (t) REVERT: C 211 SER cc_start: 0.8460 (p) cc_final: 0.8220 (m) REVERT: C 212 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: C 266 ARG cc_start: 0.7872 (ptt90) cc_final: 0.7639 (ptt90) REVERT: C 277 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7179 (mm-30) REVERT: C 323 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7639 (mtp85) REVERT: C 451 GLU cc_start: 0.8184 (tp30) cc_final: 0.7934 (mm-30) REVERT: C 458 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7449 (ttp-170) outliers start: 25 outliers final: 15 residues processed: 252 average time/residue: 0.6796 time to fit residues: 184.3079 Evaluate side-chains 264 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 384 ASN A 500 ASN B 195 ASN B 343 ASN C 396 GLN C 485 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087782 restraints weight = 17290.528| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.76 r_work: 0.3002 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12105 Z= 0.154 Angle : 0.534 9.782 16468 Z= 0.274 Chirality : 0.043 0.237 1876 Planarity : 0.004 0.040 2100 Dihedral : 8.162 70.790 2210 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.21 % Allowed : 14.68 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 aren not related in a simple way. whole: 0.71 (0.22), residues: 1433 helix: 3.52 (0.25), residues: 335 sheet: 0.82 (0.31), residues: 310 loop : -1.12 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 458 TYR 0.018 0.001 TYR B 493 PHE 0.012 0.001 PHE B 127 TRP 0.010 0.001 TRP C 236 HIS 0.012 0.002 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00369 (12060) covalent geometry : angle 0.51778 (16351) SS BOND : bond 0.00308 ( 18) SS BOND : angle 1.42379 ( 36) hydrogen bonds : bond 0.06443 ( 461) hydrogen bonds : angle 4.28123 ( 1305) link_ALPHA1-3 : bond 0.00894 ( 3) link_ALPHA1-3 : angle 1.74180 ( 9) link_ALPHA1-6 : bond 0.01030 ( 3) link_ALPHA1-6 : angle 1.39318 ( 9) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 1.65696 ( 27) link_BETA2-3 : bond 0.00048 ( 3) link_BETA2-3 : angle 2.87964 ( 9) link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.28429 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4305.63 seconds wall clock time: 74 minutes 26.83 seconds (4466.83 seconds total)