Starting phenix.real_space_refine on Tue Jun 10 16:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw6_60517/06_2025/8zw6_60517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw6_60517/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zw6_60517/06_2025/8zw6_60517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw6_60517/06_2025/8zw6_60517.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw6_60517/06_2025/8zw6_60517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw6_60517/06_2025/8zw6_60517.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.72, per 1000 atoms: 0.65 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: 3.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.61 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: 4.23 Time building geometry restraints manager: 4.13 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 502 \ or resid 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 502 or resid 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 502 or resid 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.060 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:14.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (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 TRP 0.010 0.001 TRP B 423 HIS 0.007 0.001 HIS C 473 PHE 0.007 0.001 PHE B 127 TYR 0.018 0.001 TYR C 493 ARG 0.004 0.000 ARG A 455 Details of bonding type rmsd 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) 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_ALPHA1-3 : bond 0.00411 ( 3) link_ALPHA1-3 : angle 1.56860 ( 9) hydrogen bonds : bond 0.16786 ( 461) hydrogen bonds : angle 6.45713 ( 1305) SS BOND : bond 0.00185 ( 18) SS BOND : angle 1.02382 ( 36) covalent geometry : bond 0.00315 (12060) covalent geometry : angle 0.56741 (16351) *********************** 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 : 1.224 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: 1.4697 time to fit residues: 406.3475 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 : 1.311 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 A 384 ASN B 195 ASN B 343 ASN B 384 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.085979 restraints weight = 17430.907| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.77 r_work: 0.2974 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12105 Z= 0.295 Angle : 0.640 12.295 16468 Z= 0.329 Chirality : 0.048 0.212 1876 Planarity : 0.005 0.045 2100 Dihedral : 11.280 90.506 2212 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 7.66 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1433 helix: 2.99 (0.25), residues: 334 sheet: 0.81 (0.29), residues: 301 loop : -1.15 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 236 HIS 0.014 0.003 HIS B 77 PHE 0.023 0.003 PHE B 127 TYR 0.026 0.002 TYR B 107 ARG 0.004 0.001 ARG A 323 Details of bonding type rmsd link_BETA2-3 : bond 0.01022 ( 3) link_BETA2-3 : angle 3.10462 ( 9) link_NAG-ASN : bond 0.00139 ( 9) link_NAG-ASN : angle 1.62262 ( 27) link_ALPHA1-6 : bond 0.00283 ( 3) link_ALPHA1-6 : angle 1.58335 ( 9) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 2.04784 ( 27) link_ALPHA1-3 : bond 0.00714 ( 3) link_ALPHA1-3 : angle 2.05289 ( 9) hydrogen bonds : bond 0.07645 ( 461) hydrogen bonds : angle 4.93281 ( 1305) SS BOND : bond 0.00455 ( 18) SS BOND : angle 1.23217 ( 36) covalent geometry : bond 0.00736 (12060) covalent geometry : angle 0.62330 (16351) *********************** 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 277 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7834 (t0) cc_final: 0.7500 (t0) REVERT: A 191 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 301 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8420 (ptpp) REVERT: A 458 ARG cc_start: 0.8311 (ttp80) cc_final: 0.8073 (ttp80) REVERT: A 498 LEU cc_start: 0.8400 (mm) cc_final: 0.8193 (mt) REVERT: B 33 ASP cc_start: 0.7909 (m-30) cc_final: 0.7702 (t0) REVERT: B 106 ASP cc_start: 0.7684 (t0) cc_final: 0.7342 (t0) REVERT: B 451 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: B 491 ASP cc_start: 0.8080 (m-30) cc_final: 0.7841 (m-30) REVERT: C 161 SER cc_start: 0.9013 (p) cc_final: 0.8760 (t) REVERT: C 211 SER cc_start: 0.8470 (p) cc_final: 0.8203 (m) REVERT: C 212 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: C 229 SER cc_start: 0.8821 (p) cc_final: 0.8526 (t) REVERT: C 266 ARG cc_start: 0.7844 (ptt90) cc_final: 0.7586 (ptt90) REVERT: C 342 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 451 GLU cc_start: 0.8109 (tp30) cc_final: 0.7771 (tp30) REVERT: C 481 GLU cc_start: 0.7771 (tt0) cc_final: 0.7336 (tm-30) outliers start: 30 outliers final: 14 residues processed: 255 average time/residue: 1.2901 time to fit residues: 355.8407 Evaluate side-chains 250 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 201 SER Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 320 THR 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 212 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 384 ASN B 35 GLN B 195 ASN B 343 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 = 0.3246 r_free = 0.3246 target = 0.096366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086962 restraints weight = 17535.402| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.76 r_work: 0.2980 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12105 Z= 0.194 Angle : 0.543 8.492 16468 Z= 0.281 Chirality : 0.044 0.201 1876 Planarity : 0.004 0.044 2100 Dihedral : 10.521 83.444 2210 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 11.52 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1433 helix: 3.12 (0.25), residues: 334 sheet: 0.83 (0.30), residues: 303 loop : -1.15 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.008 0.002 HIS B 77 PHE 0.015 0.002 PHE B 127 TYR 0.016 0.002 TYR B 493 ARG 0.009 0.001 ARG A 263 Details of bonding type rmsd link_BETA2-3 : bond 0.00366 ( 3) link_BETA2-3 : angle 3.47358 ( 9) link_NAG-ASN : bond 0.00112 ( 9) link_NAG-ASN : angle 1.40561 ( 27) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.73245 ( 9) link_BETA1-4 : bond 0.00338 ( 9) link_BETA1-4 : angle 1.85295 ( 27) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 1.74283 ( 9) hydrogen bonds : bond 0.06987 ( 461) hydrogen bonds : angle 4.65171 ( 1305) SS BOND : bond 0.00323 ( 18) SS BOND : angle 0.84551 ( 36) covalent geometry : bond 0.00471 (12060) covalent geometry : angle 0.52598 (16351) *********************** 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 266 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8037 (ttp80) REVERT: A 485 ASN cc_start: 0.8088 (m-40) cc_final: 0.7794 (m-40) REVERT: A 498 LEU cc_start: 0.8426 (mm) cc_final: 0.8204 (mt) REVERT: B 33 ASP cc_start: 0.7931 (m-30) cc_final: 0.7724 (t0) REVERT: B 451 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 477 ASN cc_start: 0.8372 (m110) cc_final: 0.8013 (m-40) REVERT: B 491 ASP cc_start: 0.8079 (m-30) cc_final: 0.7843 (m-30) REVERT: C 52 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8380 (mttm) REVERT: C 161 SER cc_start: 0.9003 (p) cc_final: 0.8748 (t) REVERT: C 211 SER cc_start: 0.8440 (p) cc_final: 0.8212 (m) REVERT: C 229 SER cc_start: 0.8731 (p) cc_final: 0.8490 (t) REVERT: C 266 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7643 (ptt90) REVERT: C 323 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7622 (mtp85) REVERT: C 342 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 440 ASP cc_start: 0.7787 (m-30) cc_final: 0.7550 (m-30) REVERT: C 451 GLU cc_start: 0.8143 (tp30) cc_final: 0.7908 (mm-30) REVERT: C 458 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7598 (ttp-170) outliers start: 27 outliers final: 9 residues processed: 248 average time/residue: 1.3095 time to fit residues: 350.5010 Evaluate side-chains 246 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain B residue 201 SER 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 52 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 458 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 500 ASN B 35 GLN B 195 ASN B 343 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 = 0.3260 r_free = 0.3260 target = 0.097193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087718 restraints weight = 17304.805| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.76 r_work: 0.2995 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2114 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= 0.147 Angle : 0.508 7.329 16468 Z= 0.262 Chirality : 0.043 0.216 1876 Planarity : 0.004 0.041 2100 Dihedral : 9.807 77.234 2210 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 11.92 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1433 helix: 3.31 (0.25), residues: 334 sheet: 0.95 (0.31), residues: 295 loop : -1.07 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.006 0.001 HIS B 77 PHE 0.012 0.001 PHE B 355 TYR 0.015 0.001 TYR B 493 ARG 0.006 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00065 ( 3) link_BETA2-3 : angle 2.97164 ( 9) link_NAG-ASN : bond 0.00134 ( 9) link_NAG-ASN : angle 1.23671 ( 27) link_ALPHA1-6 : bond 0.00669 ( 3) link_ALPHA1-6 : angle 1.68858 ( 9) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.68411 ( 27) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 1.88348 ( 9) hydrogen bonds : bond 0.06465 ( 461) hydrogen bonds : angle 4.45107 ( 1305) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.73739 ( 36) covalent geometry : bond 0.00349 (12060) covalent geometry : angle 0.49302 (16351) *********************** 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 270 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8720 (ttm170) cc_final: 0.8254 (ttp80) REVERT: A 403 GLU cc_start: 0.7344 (tp30) cc_final: 0.7048 (tp30) REVERT: A 458 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7922 (ttp80) REVERT: A 485 ASN cc_start: 0.8126 (m-40) cc_final: 0.7828 (m-40) REVERT: A 498 LEU cc_start: 0.8415 (mm) cc_final: 0.8192 (mt) REVERT: B 33 ASP cc_start: 0.7949 (m-30) cc_final: 0.7736 (t0) REVERT: B 477 ASN cc_start: 0.8356 (m110) cc_final: 0.8099 (m-40) REVERT: B 491 ASP cc_start: 0.8086 (m-30) cc_final: 0.7851 (m-30) REVERT: C 52 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: C 161 SER cc_start: 0.8979 (p) cc_final: 0.8719 (t) REVERT: C 207 SER cc_start: 0.8588 (p) cc_final: 0.8346 (m) REVERT: C 211 SER cc_start: 0.8436 (p) cc_final: 0.8190 (m) REVERT: C 212 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: C 229 SER cc_start: 0.8688 (p) cc_final: 0.8474 (t) REVERT: C 266 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7586 (ptt90) REVERT: C 323 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7609 (mtp85) REVERT: C 342 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 440 ASP cc_start: 0.7819 (m-30) cc_final: 0.7566 (m-30) REVERT: C 451 GLU cc_start: 0.8125 (tp30) cc_final: 0.7881 (mm-30) REVERT: C 458 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7552 (ttp-170) outliers start: 27 outliers final: 13 residues processed: 252 average time/residue: 1.4183 time to fit residues: 386.3636 Evaluate side-chains 251 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 369 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 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 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU 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 60 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 396 GLN 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 = 0.097287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087814 restraints weight = 17222.979| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.76 r_work: 0.2999 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12105 Z= 0.139 Angle : 0.499 8.289 16468 Z= 0.257 Chirality : 0.043 0.229 1876 Planarity : 0.004 0.040 2100 Dihedral : 9.348 72.318 2210 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.21 % Allowed : 12.63 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1433 helix: 3.48 (0.25), residues: 335 sheet: 0.84 (0.30), residues: 310 loop : -1.06 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 236 HIS 0.014 0.002 HIS C 357 PHE 0.013 0.001 PHE B 355 TYR 0.016 0.001 TYR B 493 ARG 0.006 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00079 ( 3) link_BETA2-3 : angle 2.98250 ( 9) link_NAG-ASN : bond 0.00158 ( 9) link_NAG-ASN : angle 1.20543 ( 27) link_ALPHA1-6 : bond 0.00779 ( 3) link_ALPHA1-6 : angle 1.57606 ( 9) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 1.62753 ( 27) link_ALPHA1-3 : bond 0.00934 ( 3) link_ALPHA1-3 : angle 1.89399 ( 9) hydrogen bonds : bond 0.06317 ( 461) hydrogen bonds : angle 4.34419 ( 1305) SS BOND : bond 0.00233 ( 18) SS BOND : angle 0.74079 ( 36) covalent geometry : bond 0.00328 (12060) covalent geometry : angle 0.48457 (16351) *********************** 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 268 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8715 (ttm170) cc_final: 0.8249 (ttp80) REVERT: A 298 ASN cc_start: 0.8459 (t0) cc_final: 0.8183 (t0) REVERT: A 301 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8398 (ptpp) REVERT: A 403 GLU cc_start: 0.7351 (tp30) cc_final: 0.7072 (tp30) REVERT: A 458 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7949 (ttp80) REVERT: A 485 ASN cc_start: 0.8136 (m-40) cc_final: 0.7846 (m-40) REVERT: A 498 LEU cc_start: 0.8409 (mm) cc_final: 0.8196 (mt) REVERT: B 314 ASN cc_start: 0.8136 (p0) cc_final: 0.7495 (t0) REVERT: B 491 ASP cc_start: 0.8109 (m-30) cc_final: 0.7867 (m-30) REVERT: C 52 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8406 (mttm) REVERT: C 161 SER cc_start: 0.8968 (p) cc_final: 0.8696 (t) REVERT: C 207 SER cc_start: 0.8568 (p) cc_final: 0.8358 (m) REVERT: C 211 SER cc_start: 0.8440 (p) cc_final: 0.8199 (m) REVERT: C 212 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: C 266 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7591 (ptt90) REVERT: C 323 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7615 (mtp85) REVERT: C 440 ASP cc_start: 0.7832 (m-30) cc_final: 0.7563 (m-30) REVERT: C 451 GLU cc_start: 0.8155 (tp30) cc_final: 0.7902 (mm-30) outliers start: 28 outliers final: 15 residues processed: 249 average time/residue: 1.6152 time to fit residues: 433.7698 Evaluate side-chains 255 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 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 A residue 458 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 369 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 C residue 33 ASP 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 323 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 396 GLN C 485 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087284 restraints weight = 17534.444| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.78 r_work: 0.2983 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2309 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= 0.180 Angle : 0.529 9.427 16468 Z= 0.271 Chirality : 0.044 0.250 1876 Planarity : 0.004 0.041 2100 Dihedral : 9.105 70.133 2210 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.45 % Allowed : 13.26 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1433 helix: 3.48 (0.25), residues: 334 sheet: 0.92 (0.31), residues: 293 loop : -1.05 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.012 0.002 HIS C 357 PHE 0.018 0.002 PHE B 127 TYR 0.017 0.002 TYR B 493 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00111 ( 3) link_BETA2-3 : angle 3.13810 ( 9) link_NAG-ASN : bond 0.00169 ( 9) link_NAG-ASN : angle 1.29872 ( 27) link_ALPHA1-6 : bond 0.00810 ( 3) link_ALPHA1-6 : angle 1.42731 ( 9) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 1.70845 ( 27) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.88274 ( 9) hydrogen bonds : bond 0.06647 ( 461) hydrogen bonds : angle 4.36183 ( 1305) SS BOND : bond 0.00298 ( 18) SS BOND : angle 0.77990 ( 36) covalent geometry : bond 0.00439 (12060) covalent geometry : angle 0.51378 (16351) *********************** 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 273 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8328 (ttm) REVERT: A 203 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8263 (ttp80) REVERT: A 298 ASN cc_start: 0.8492 (t0) cc_final: 0.8225 (t0) REVERT: A 301 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: A 403 GLU cc_start: 0.7397 (tp30) cc_final: 0.7115 (tp30) REVERT: A 458 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: A 485 ASN cc_start: 0.8163 (m-40) cc_final: 0.7865 (m-40) REVERT: A 498 LEU cc_start: 0.8417 (mm) cc_final: 0.8212 (mt) REVERT: B 314 ASN cc_start: 0.8109 (p0) cc_final: 0.7488 (t0) REVERT: B 346 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 348 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8123 (ttm) REVERT: C 52 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8416 (mttm) REVERT: C 161 SER cc_start: 0.8972 (p) cc_final: 0.8691 (t) REVERT: C 211 SER cc_start: 0.8454 (p) cc_final: 0.8211 (m) REVERT: C 212 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: C 266 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7607 (ptt90) REVERT: C 323 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7656 (mtp85) REVERT: C 451 GLU cc_start: 0.8186 (tp30) cc_final: 0.7820 (tp30) outliers start: 31 outliers final: 14 residues processed: 253 average time/residue: 1.8649 time to fit residues: 509.8372 Evaluate side-chains 253 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 301 LYS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain B residue 201 SER 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 444 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN B 343 ASN C 396 GLN C 485 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087646 restraints weight = 17487.759| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.79 r_work: 0.3004 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12105 Z= 0.139 Angle : 0.497 8.712 16468 Z= 0.255 Chirality : 0.043 0.243 1876 Planarity : 0.004 0.039 2100 Dihedral : 8.615 70.259 2210 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.21 % Allowed : 14.29 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1433 helix: 3.59 (0.25), residues: 336 sheet: 0.84 (0.30), residues: 310 loop : -1.05 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.011 0.002 HIS C 357 PHE 0.012 0.001 PHE B 355 TYR 0.016 0.001 TYR B 493 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00050 ( 3) link_BETA2-3 : angle 2.87582 ( 9) link_NAG-ASN : bond 0.00164 ( 9) link_NAG-ASN : angle 1.21991 ( 27) link_ALPHA1-6 : bond 0.00959 ( 3) link_ALPHA1-6 : angle 1.44883 ( 9) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 1.57482 ( 27) link_ALPHA1-3 : bond 0.00961 ( 3) link_ALPHA1-3 : angle 1.84809 ( 9) hydrogen bonds : bond 0.06304 ( 461) hydrogen bonds : angle 4.28621 ( 1305) SS BOND : bond 0.00231 ( 18) SS BOND : angle 0.75768 ( 36) covalent geometry : bond 0.00328 (12060) covalent geometry : angle 0.48288 (16351) *********************** 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 267 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 203 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8249 (ttp80) REVERT: A 298 ASN cc_start: 0.8455 (t0) cc_final: 0.8188 (t0) REVERT: A 301 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8406 (ptpp) REVERT: A 403 GLU cc_start: 0.7375 (tp30) cc_final: 0.7029 (tp30) REVERT: A 458 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7925 (ttp80) REVERT: A 485 ASN cc_start: 0.8161 (m-40) cc_final: 0.7870 (m-40) REVERT: A 498 LEU cc_start: 0.8396 (mm) cc_final: 0.8186 (mt) REVERT: B 240 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8075 (mttm) REVERT: B 314 ASN cc_start: 0.8090 (p0) cc_final: 0.7497 (t0) REVERT: B 346 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 52 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: C 103 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7953 (p0) REVERT: C 161 SER cc_start: 0.8947 (p) cc_final: 0.8653 (t) REVERT: C 211 SER cc_start: 0.8444 (p) cc_final: 0.8207 (m) REVERT: C 212 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: C 266 ARG cc_start: 0.7854 (ptt90) cc_final: 0.7568 (ptt90) REVERT: C 277 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 323 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7626 (mtp85) REVERT: C 357 HIS cc_start: 0.8426 (p-80) cc_final: 0.8175 (p-80) REVERT: C 451 GLU cc_start: 0.8174 (tp30) cc_final: 0.7924 (mm-30) outliers start: 28 outliers final: 15 residues processed: 249 average time/residue: 1.2962 time to fit residues: 348.7081 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 : 1.390 ------------------------------------------------------------------------------- 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 201 SER Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain B residue 201 SER 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 C residue 52 LYS 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 301 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 396 GLN 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 = 0.097411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087887 restraints weight = 17455.678| |-----------------------------------------------------------------------------| 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: 3.58 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12105 Z= 0.148 Angle : 0.507 8.666 16468 Z= 0.260 Chirality : 0.043 0.244 1876 Planarity : 0.004 0.039 2100 Dihedral : 8.395 69.985 2210 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.45 % Allowed : 14.29 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1433 helix: 3.57 (0.25), residues: 337 sheet: 0.83 (0.30), residues: 310 loop : -1.06 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 236 HIS 0.011 0.002 HIS C 357 PHE 0.013 0.001 PHE B 355 TYR 0.019 0.001 TYR B 493 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00026 ( 3) link_BETA2-3 : angle 2.91106 ( 9) link_NAG-ASN : bond 0.00184 ( 9) link_NAG-ASN : angle 1.23163 ( 27) link_ALPHA1-6 : bond 0.00974 ( 3) link_ALPHA1-6 : angle 1.40606 ( 9) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.60555 ( 27) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.85027 ( 9) hydrogen bonds : bond 0.06346 ( 461) hydrogen bonds : angle 4.26631 ( 1305) SS BOND : bond 0.00245 ( 18) SS BOND : angle 0.79836 ( 36) covalent geometry : bond 0.00352 (12060) covalent geometry : angle 0.49334 (16351) *********************** 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 272 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: A 203 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8254 (ttp80) REVERT: A 298 ASN cc_start: 0.8457 (t0) cc_final: 0.8193 (t0) REVERT: A 301 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8404 (ptpp) REVERT: A 403 GLU cc_start: 0.7403 (tp30) cc_final: 0.7083 (tp30) REVERT: A 458 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7920 (ttp80) REVERT: A 485 ASN cc_start: 0.8158 (m-40) cc_final: 0.7873 (m-40) REVERT: A 498 LEU cc_start: 0.8416 (mm) cc_final: 0.8215 (mt) REVERT: B 240 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8153 (mttm) REVERT: B 314 ASN cc_start: 0.8104 (p0) cc_final: 0.7539 (t0) REVERT: C 52 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (mttm) REVERT: C 103 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7921 (p0) REVERT: C 161 SER cc_start: 0.8932 (p) cc_final: 0.8630 (t) REVERT: C 211 SER cc_start: 0.8454 (p) cc_final: 0.8214 (m) REVERT: C 212 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: C 266 ARG cc_start: 0.7850 (ptt90) cc_final: 0.7575 (ptt90) REVERT: C 277 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7147 (mm-30) REVERT: C 323 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7634 (mtp85) REVERT: C 357 HIS cc_start: 0.8426 (p-80) cc_final: 0.8202 (p-80) REVERT: C 451 GLU cc_start: 0.8164 (tp30) cc_final: 0.7910 (tp30) outliers start: 31 outliers final: 20 residues processed: 253 average time/residue: 1.3029 time to fit residues: 355.6416 Evaluate side-chains 269 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 LYS 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 194 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain B residue 201 SER 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 C residue 52 LYS 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 262 ILE Chi-restraints excluded: chain C residue 301 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 chunk 3 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.096893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087414 restraints weight = 17359.668| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.78 r_work: 0.2998 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2466 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= 0.169 Angle : 0.530 8.830 16468 Z= 0.271 Chirality : 0.043 0.245 1876 Planarity : 0.004 0.039 2100 Dihedral : 8.289 70.270 2210 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.37 % Allowed : 15.00 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1433 helix: 3.50 (0.25), residues: 336 sheet: 0.85 (0.30), residues: 308 loop : -1.08 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 236 HIS 0.010 0.002 HIS C 357 PHE 0.014 0.002 PHE B 127 TYR 0.019 0.001 TYR B 493 ARG 0.008 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00053 ( 3) link_BETA2-3 : angle 2.99555 ( 9) link_NAG-ASN : bond 0.00189 ( 9) link_NAG-ASN : angle 1.29822 ( 27) link_ALPHA1-6 : bond 0.01019 ( 3) link_ALPHA1-6 : angle 1.39177 ( 9) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.68652 ( 27) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 1.78258 ( 9) hydrogen bonds : bond 0.06561 ( 461) hydrogen bonds : angle 4.29671 ( 1305) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.84629 ( 36) covalent geometry : bond 0.00409 (12060) covalent geometry : angle 0.51560 (16351) *********************** 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 275 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: A 203 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8273 (ttp80) REVERT: A 298 ASN cc_start: 0.8461 (t0) cc_final: 0.8197 (t0) REVERT: A 301 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: A 314 ASN cc_start: 0.8017 (p0) cc_final: 0.7692 (t0) REVERT: A 403 GLU cc_start: 0.7462 (tp30) cc_final: 0.7128 (tp30) REVERT: A 485 ASN cc_start: 0.8154 (m-40) cc_final: 0.7865 (m-40) REVERT: B 240 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8177 (mttm) REVERT: B 314 ASN cc_start: 0.8113 (p0) cc_final: 0.7569 (t0) REVERT: B 348 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8099 (ttm) REVERT: C 52 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8400 (mttm) REVERT: C 161 SER cc_start: 0.8928 (p) cc_final: 0.8620 (t) REVERT: C 211 SER cc_start: 0.8439 (p) cc_final: 0.8217 (m) REVERT: C 212 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: C 266 ARG cc_start: 0.7867 (ptt90) cc_final: 0.7587 (ptt90) REVERT: C 277 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 323 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: C 357 HIS cc_start: 0.8439 (p-80) cc_final: 0.8212 (p-80) REVERT: C 451 GLU cc_start: 0.8181 (tp30) cc_final: 0.7946 (tp30) outliers start: 30 outliers final: 19 residues processed: 256 average time/residue: 1.3077 time to fit residues: 361.9081 Evaluate side-chains 271 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 113 LEU 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 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 201 SER 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 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 244 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 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 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 = 0.3243 r_free = 0.3243 target = 0.096230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086793 restraints weight = 17442.291| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.78 r_work: 0.2989 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12105 Z= 0.222 Angle : 0.570 9.909 16468 Z= 0.291 Chirality : 0.045 0.256 1876 Planarity : 0.004 0.040 2100 Dihedral : 8.407 70.979 2210 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 15.00 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1433 helix: 3.34 (0.25), residues: 336 sheet: 0.84 (0.31), residues: 303 loop : -1.11 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.011 0.002 HIS B 357 PHE 0.018 0.002 PHE B 127 TYR 0.020 0.002 TYR B 493 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_BETA2-3 : bond 0.00064 ( 3) link_BETA2-3 : angle 3.22455 ( 9) link_NAG-ASN : bond 0.00229 ( 9) link_NAG-ASN : angle 1.44819 ( 27) link_ALPHA1-6 : bond 0.00994 ( 3) link_ALPHA1-6 : angle 1.39347 ( 9) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.86049 ( 27) link_ALPHA1-3 : bond 0.00885 ( 3) link_ALPHA1-3 : angle 1.74259 ( 9) hydrogen bonds : bond 0.07035 ( 461) hydrogen bonds : angle 4.38421 ( 1305) SS BOND : bond 0.00337 ( 18) SS BOND : angle 0.92015 ( 36) covalent geometry : bond 0.00547 (12060) covalent geometry : angle 0.55509 (16351) ********************** 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 275 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: A 203 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8289 (ttp80) REVERT: A 298 ASN cc_start: 0.8484 (t0) cc_final: 0.8226 (t0) REVERT: A 301 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8401 (ptpp) REVERT: A 314 ASN cc_start: 0.8042 (p0) cc_final: 0.7738 (t0) REVERT: A 403 GLU cc_start: 0.7499 (tp30) cc_final: 0.7174 (tp30) REVERT: A 485 ASN cc_start: 0.8172 (m-40) cc_final: 0.7870 (m-40) REVERT: B 240 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8224 (mttm) REVERT: B 314 ASN cc_start: 0.8122 (p0) cc_final: 0.7588 (t0) REVERT: B 348 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8182 (ttm) REVERT: C 52 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8408 (mttm) REVERT: C 103 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7891 (p0) REVERT: C 106 ASP cc_start: 0.7844 (m-30) cc_final: 0.7632 (t0) REVERT: C 161 SER cc_start: 0.8919 (p) cc_final: 0.8610 (t) REVERT: C 211 SER cc_start: 0.8456 (p) cc_final: 0.8227 (m) REVERT: C 212 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8581 (pt0) REVERT: C 266 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7654 (ptt90) REVERT: C 277 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7186 (mm-30) REVERT: C 323 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7672 (mtp85) REVERT: C 357 HIS cc_start: 0.8459 (p-80) cc_final: 0.8221 (p-80) REVERT: C 416 GLU cc_start: 0.7840 (tp30) cc_final: 0.7627 (mm-30) REVERT: C 451 GLU cc_start: 0.8151 (tp30) cc_final: 0.7884 (tp30) outliers start: 30 outliers final: 21 residues processed: 256 average time/residue: 1.3480 time to fit residues: 372.8711 Evaluate side-chains 271 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 113 LEU 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 301 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 369 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 C residue 52 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 195 ASN 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 244 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 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 378 GLN A 384 ASN A 456 GLN A 500 ASN B 195 ASN B 343 ASN C 396 GLN C 485 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087822 restraints weight = 17283.594| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.76 r_work: 0.3013 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12105 Z= 0.139 Angle : 0.508 8.374 16468 Z= 0.261 Chirality : 0.042 0.231 1876 Planarity : 0.004 0.039 2100 Dihedral : 8.108 70.944 2210 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.05 % Allowed : 15.47 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1433 helix: 3.49 (0.25), residues: 338 sheet: 0.89 (0.31), residues: 308 loop : -1.08 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 236 HIS 0.011 0.002 HIS B 357 PHE 0.012 0.001 PHE A 127 TYR 0.019 0.001 TYR B 493 ARG 0.008 0.000 ARG A 458 Details of bonding type rmsd link_BETA2-3 : bond 0.00065 ( 3) link_BETA2-3 : angle 2.81279 ( 9) link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 1.27765 ( 27) link_ALPHA1-6 : bond 0.00997 ( 3) link_ALPHA1-6 : angle 1.37722 ( 9) link_BETA1-4 : bond 0.00436 ( 9) link_BETA1-4 : angle 1.62305 ( 27) link_ALPHA1-3 : bond 0.00880 ( 3) link_ALPHA1-3 : angle 1.68966 ( 9) hydrogen bonds : bond 0.06394 ( 461) hydrogen bonds : angle 4.28713 ( 1305) SS BOND : bond 0.00237 ( 18) SS BOND : angle 0.82284 ( 36) covalent geometry : bond 0.00327 (12060) covalent geometry : angle 0.49430 (16351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9640.24 seconds wall clock time: 169 minutes 16.00 seconds (10156.00 seconds total)