Starting phenix.real_space_refine on Wed Sep 17 22:46:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw7_60518/09_2025/8zw7_60518.cif" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 7387 2.51 5 N 2050 2.21 5 O 2402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11896 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3829 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3827 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} 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: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3835 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.54, per 1000 atoms: 0.30 Number of scatterers: 11896 At special positions: 0 Unit cell: (88.4, 85, 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 2402 8.00 N 2050 7.00 C 7387 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 " BETA2-6 " GAL J 1 " - " SIA J 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL K 1 " - " SIA K 2 " " GAL L 1 " - " SIA L 2 " NAG-ASN " NAG A 601 " - " ASN A 40 " " NAG B 601 " - " ASN B 40 " " NAG C 601 " - " ASN C 40 " " NAG D 1 " - " ASN A 167 " " NAG E 1 " - " ASN A 287 " " NAG F 1 " - " ASN B 167 " " NAG G 1 " - " ASN B 287 " " NAG H 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 287 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 540.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2702 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 36 sheets defined 27.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.607A pdb=" N ASP A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 406 through 457 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 489 through 502 removed outlier: 4.417A pdb=" N TYR A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 75 through 82 removed outlier: 5.241A pdb=" N VAL B 80 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 82 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 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: 3.569A 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 489 through 502 removed outlier: 4.422A pdb=" N TYR B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP B 495 " --> pdb=" O ASP B 491 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 75 through 82 removed outlier: 5.220A pdb=" N VAL C 80 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 118 Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.614A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.553A pdb=" N VAL C 386 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 457 removed outlier: 3.511A pdb=" N LEU C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 486 Processing helix chain 'C' and resid 490 through 502 removed outlier: 4.630A pdb=" N ASP C 495 " --> pdb=" O ASP C 491 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLU C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 368 removed outlier: 4.716A pdb=" N TYR A 353 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 18 " --> pdb=" O GLY A 354 " (cutoff:3.500A) 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: 5.964A pdb=" N ILE A 53 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS A 279 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.783A 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: 6.060A 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: 6.467A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE A 181 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 7.879A 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: 6.467A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.942A 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: 4.836A pdb=" N CYS A 141 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.651A 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 removed outlier: 5.133A pdb=" N ARG A 203 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.395A pdb=" N ASN A 391 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 364 through 368 removed outlier: 3.525A pdb=" N HIS B 357 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 353 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 470 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.500A 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: 6.016A pdb=" N ILE B 53 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N CYS B 279 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.730A 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: 6.836A pdb=" N LEU B 61 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 89 " --> pdb=" O MET B 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 103 removed outlier: 4.961A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 102 through 103 removed outlier: 7.893A pdb=" N ILE B 181 " --> pdb=" O PRO B 256 " (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: 4.837A pdb=" N CYS B 141 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.818A 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 290 removed outlier: 3.505A pdb=" N ILE B 290 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS B 283 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS B 307 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN B 391 " --> pdb=" O CYS B 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 363 through 365 removed outlier: 3.614A 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: 5.993A pdb=" N ILE C 53 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS C 279 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.765A 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: 6.781A pdb=" N LEU C 61 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.032A 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 102 through 103 removed outlier: 4.939A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.860A pdb=" N ILE C 181 " --> pdb=" O PRO C 256 " (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: 4.893A pdb=" N CYS C 141 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.610A 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: 4.384A pdb=" N ASN C 391 " --> pdb=" O CYS C 307 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3936 1.34 - 1.46: 2634 1.46 - 1.58: 5485 1.58 - 1.69: 3 1.69 - 1.81: 78 Bond restraints: 12136 Sorted by residual: bond pdb=" C6 GAL J 1 " pdb=" O6 GAL J 1 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C6 GAL L 1 " pdb=" O6 GAL L 1 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C6 GAL K 1 " pdb=" O6 GAL K 1 " ideal model delta sigma weight residual 1.407 1.375 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 MAN D 4 " pdb=" C2 MAN D 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C5 GAL J 1 " pdb=" O5 GAL J 1 " ideal model delta sigma weight residual 1.412 1.442 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 16122 1.50 - 3.01: 233 3.01 - 4.51: 66 4.51 - 6.01: 21 6.01 - 7.52: 13 Bond angle restraints: 16455 Sorted by residual: angle pdb=" CA GLU C 388 " pdb=" CB GLU C 388 " pdb=" CG GLU C 388 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C GLU C 388 " pdb=" CA GLU C 388 " pdb=" CB GLU C 388 " ideal model delta sigma weight residual 109.54 114.08 -4.54 1.84e+00 2.95e-01 6.09e+00 angle pdb=" CB ILE C 349 " pdb=" CG1 ILE C 349 " pdb=" CD1 ILE C 349 " ideal model delta sigma weight residual 113.80 118.97 -5.17 2.10e+00 2.27e-01 6.07e+00 angle pdb=" CA ILE C 349 " pdb=" CB ILE C 349 " pdb=" CG1 ILE C 349 " ideal model delta sigma weight residual 110.40 114.50 -4.10 1.70e+00 3.46e-01 5.82e+00 angle pdb=" CB GLN C 358 " pdb=" CG GLN C 358 " pdb=" CD GLN C 358 " ideal model delta sigma weight residual 112.60 116.44 -3.84 1.70e+00 3.46e-01 5.10e+00 ... (remaining 16450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 7044 21.99 - 43.98: 547 43.98 - 65.97: 75 65.97 - 87.95: 43 87.95 - 109.94: 15 Dihedral angle restraints: 7724 sinusoidal: 3524 harmonic: 4200 Sorted by residual: 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 288.71 178.77 109.94 1 3.00e+01 1.11e-03 1.43e+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 288.71 178.90 109.81 1 3.00e+01 1.11e-03 1.43e+01 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 288.71 179.45 109.26 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1599 0.055 - 0.111: 236 0.111 - 0.166: 48 0.166 - 0.222: 0 0.222 - 0.277: 3 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C2 SIA L 2 " pdb=" O6 GAL L 1 " pdb=" C1 SIA L 2 " pdb=" O6 SIA L 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.63 0.13 2.00e-02 2.50e+03 4.54e+01 chirality pdb=" C2 SIA J 2 " pdb=" O6 GAL J 1 " pdb=" C1 SIA J 2 " pdb=" O6 SIA J 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.63 0.13 2.00e-02 2.50e+03 4.11e+01 chirality pdb=" C2 SIA K 2 " pdb=" O6 GAL K 1 " pdb=" C1 SIA K 2 " pdb=" O6 SIA K 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.62 0.12 2.00e-02 2.50e+03 3.70e+01 ... (remaining 1883 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 75 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 76 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 404 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C VAL C 404 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL C 404 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU C 405 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 285 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO C 286 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " -0.016 5.00e-02 4.00e+02 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 567 2.73 - 3.27: 10645 3.27 - 3.81: 19555 3.81 - 4.36: 23446 4.36 - 4.90: 40871 Nonbonded interactions: 95084 Sorted by model distance: nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.185 3.120 nonbonded pdb=" N GLU B 346 " pdb=" OE1 GLU B 346 " model vdw 2.231 3.120 nonbonded pdb=" ND2 ASN B 359 " pdb=" O CYS B 475 " model vdw 2.251 3.120 nonbonded pdb=" OG1 THR A 285 " pdb=" O GLY A 288 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU A 192 " pdb=" O9 SIA J 2 " model vdw 2.274 3.040 ... (remaining 95079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 462 or (resid 463 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 464 through 601) \ ) selection = (chain 'B' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 601)) selection = (chain 'C' and (resid 12 through 329 or resid 336 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 thr \ ough 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: 2.140 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 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 0.062 12181 Z= 0.156 Angle : 0.598 19.624 16572 Z= 0.259 Chirality : 0.043 0.277 1886 Planarity : 0.003 0.029 2115 Dihedral : 16.852 109.941 4968 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.39 % Allowed : 10.99 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.22), residues: 1444 helix: 4.31 (0.24), residues: 337 sheet: 0.85 (0.28), residues: 337 loop : -0.58 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 458 TYR 0.011 0.001 TYR C 493 PHE 0.005 0.001 PHE C 355 TRP 0.010 0.001 TRP B 423 HIS 0.002 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00305 (12136) covalent geometry : angle 0.53836 (16455) SS BOND : bond 0.00116 ( 18) SS BOND : angle 0.43610 ( 36) hydrogen bonds : bond 0.17453 ( 478) hydrogen bonds : angle 6.52291 ( 1380) glycosidic custom : bond 0.06118 ( 3) glycosidic custom : angle 10.68582 ( 9) link_ALPHA1-3 : bond 0.00380 ( 3) link_ALPHA1-3 : angle 1.55588 ( 9) link_ALPHA1-6 : bond 0.00368 ( 3) link_ALPHA1-6 : angle 1.53031 ( 9) link_BETA1-4 : bond 0.00274 ( 9) link_BETA1-4 : angle 1.43328 ( 27) link_NAG-ASN : bond 0.00070 ( 9) link_NAG-ASN : angle 0.97524 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.601 Fit side-chains outliers start: 5 outliers final: 6 residues processed: 76 average time/residue: 0.8084 time to fit residues: 65.9341 Evaluate side-chains 74 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 444 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.065647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.048461 restraints weight = 23579.675| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 2.69 r_work: 0.2411 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2293 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12181 Z= 0.125 Angle : 0.478 7.558 16572 Z= 0.248 Chirality : 0.041 0.162 1886 Planarity : 0.003 0.031 2115 Dihedral : 11.143 89.779 2231 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 10.20 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.22), residues: 1444 helix: 4.40 (0.24), residues: 336 sheet: 0.79 (0.28), residues: 338 loop : -0.59 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 222 TYR 0.009 0.001 TYR A 107 PHE 0.008 0.001 PHE B 355 TRP 0.007 0.001 TRP C 423 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00281 (12136) covalent geometry : angle 0.46611 (16455) SS BOND : bond 0.00128 ( 18) SS BOND : angle 0.41479 ( 36) hydrogen bonds : bond 0.05957 ( 478) hydrogen bonds : angle 5.00627 ( 1380) glycosidic custom : bond 0.00426 ( 3) glycosidic custom : angle 0.62513 ( 9) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 2.35468 ( 9) link_ALPHA1-6 : bond 0.00361 ( 3) link_ALPHA1-6 : angle 2.23475 ( 9) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.73407 ( 27) link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 0.94544 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.492 Fit side-chains REVERT: A 459 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7595 (pm20) outliers start: 8 outliers final: 1 residues processed: 77 average time/residue: 0.7580 time to fit residues: 62.8282 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.062960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.045684 restraints weight = 23988.655| |-----------------------------------------------------------------------------| r_work (start): 0.2478 rms_B_bonded: 2.72 r_work: 0.2345 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12181 Z= 0.306 Angle : 0.593 8.888 16572 Z= 0.308 Chirality : 0.047 0.160 1886 Planarity : 0.004 0.037 2115 Dihedral : 10.990 88.560 2221 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.26 % Allowed : 10.68 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.21), residues: 1444 helix: 4.01 (0.24), residues: 336 sheet: 0.75 (0.28), residues: 328 loop : -0.91 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.011 0.002 TYR B 163 PHE 0.013 0.001 PHE C 355 TRP 0.008 0.001 TRP C 423 HIS 0.007 0.002 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00735 (12136) covalent geometry : angle 0.57984 (16455) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.60516 ( 36) hydrogen bonds : bond 0.07330 ( 478) hydrogen bonds : angle 4.96741 ( 1380) glycosidic custom : bond 0.00284 ( 3) glycosidic custom : angle 0.67743 ( 9) link_ALPHA1-3 : bond 0.00724 ( 3) link_ALPHA1-3 : angle 2.40296 ( 9) link_ALPHA1-6 : bond 0.00270 ( 3) link_ALPHA1-6 : angle 2.22534 ( 9) link_BETA1-4 : bond 0.00217 ( 9) link_BETA1-4 : angle 2.23012 ( 27) link_NAG-ASN : bond 0.00320 ( 9) link_NAG-ASN : angle 1.41998 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.398 Fit side-chains REVERT: C 33 ASP cc_start: 0.8497 (m-30) cc_final: 0.8280 (m-30) outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 0.6366 time to fit residues: 53.8147 Evaluate side-chains 74 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 134 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.064762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.047593 restraints weight = 23552.964| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 2.69 r_work: 0.2387 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2270 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12181 Z= 0.134 Angle : 0.482 6.910 16572 Z= 0.250 Chirality : 0.042 0.176 1886 Planarity : 0.003 0.036 2115 Dihedral : 10.394 89.022 2221 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 11.07 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1444 helix: 4.24 (0.24), residues: 336 sheet: 0.82 (0.28), residues: 332 loop : -0.82 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 222 TYR 0.009 0.001 TYR C 493 PHE 0.009 0.001 PHE C 355 TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00309 (12136) covalent geometry : angle 0.47112 (16455) SS BOND : bond 0.00127 ( 18) SS BOND : angle 0.41758 ( 36) hydrogen bonds : bond 0.06075 ( 478) hydrogen bonds : angle 4.60973 ( 1380) glycosidic custom : bond 0.00127 ( 3) glycosidic custom : angle 0.47871 ( 9) link_ALPHA1-3 : bond 0.00930 ( 3) link_ALPHA1-3 : angle 2.07374 ( 9) link_ALPHA1-6 : bond 0.00502 ( 3) link_ALPHA1-6 : angle 2.18355 ( 9) link_BETA1-4 : bond 0.00236 ( 9) link_BETA1-4 : angle 1.71332 ( 27) link_NAG-ASN : bond 0.00086 ( 9) link_NAG-ASN : angle 1.07791 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.558 Fit side-chains REVERT: A 197 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7705 (m-80) outliers start: 15 outliers final: 3 residues processed: 78 average time/residue: 0.6933 time to fit residues: 58.5680 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.047893 restraints weight = 23532.736| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 2.64 r_work: 0.2388 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2272 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12181 Z= 0.153 Angle : 0.497 8.131 16572 Z= 0.255 Chirality : 0.042 0.185 1886 Planarity : 0.003 0.036 2115 Dihedral : 10.080 89.944 2221 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.94 % Allowed : 11.38 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1444 helix: 4.27 (0.24), residues: 336 sheet: 0.77 (0.28), residues: 334 loop : -0.80 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.007 0.001 TYR C 493 PHE 0.010 0.001 PHE C 355 TRP 0.008 0.001 TRP C 423 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00361 (12136) covalent geometry : angle 0.48598 (16455) SS BOND : bond 0.00140 ( 18) SS BOND : angle 0.41291 ( 36) hydrogen bonds : bond 0.06122 ( 478) hydrogen bonds : angle 4.53829 ( 1380) glycosidic custom : bond 0.00083 ( 3) glycosidic custom : angle 0.44408 ( 9) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 2.21373 ( 9) link_ALPHA1-6 : bond 0.00510 ( 3) link_ALPHA1-6 : angle 2.18183 ( 9) link_BETA1-4 : bond 0.00206 ( 9) link_BETA1-4 : angle 1.78021 ( 27) link_NAG-ASN : bond 0.00118 ( 9) link_NAG-ASN : angle 1.12449 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.402 Fit side-chains REVERT: A 197 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7720 (m-80) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 0.7003 time to fit residues: 56.6930 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.064459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.047530 restraints weight = 23584.022| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 2.65 r_work: 0.2378 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9228 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12181 Z= 0.180 Angle : 0.514 7.821 16572 Z= 0.265 Chirality : 0.043 0.191 1886 Planarity : 0.003 0.036 2115 Dihedral : 9.967 89.660 2221 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.78 % Allowed : 11.70 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1444 helix: 4.22 (0.24), residues: 336 sheet: 0.76 (0.28), residues: 332 loop : -0.86 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.007 0.001 TYR B 163 PHE 0.010 0.001 PHE C 355 TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00428 (12136) covalent geometry : angle 0.50268 (16455) SS BOND : bond 0.00156 ( 18) SS BOND : angle 0.44323 ( 36) hydrogen bonds : bond 0.06309 ( 478) hydrogen bonds : angle 4.56350 ( 1380) glycosidic custom : bond 0.00085 ( 3) glycosidic custom : angle 0.47735 ( 9) link_ALPHA1-3 : bond 0.00850 ( 3) link_ALPHA1-3 : angle 2.22705 ( 9) link_ALPHA1-6 : bond 0.00483 ( 3) link_ALPHA1-6 : angle 2.19501 ( 9) link_BETA1-4 : bond 0.00194 ( 9) link_BETA1-4 : angle 1.82177 ( 27) link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 1.18403 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.372 Fit side-chains REVERT: A 197 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: C 33 ASP cc_start: 0.8464 (m-30) cc_final: 0.8249 (m-30) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.6486 time to fit residues: 52.8735 Evaluate side-chains 73 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.048699 restraints weight = 23434.232| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 2.64 r_work: 0.2409 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2293 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9191 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12181 Z= 0.120 Angle : 0.478 7.488 16572 Z= 0.245 Chirality : 0.041 0.203 1886 Planarity : 0.003 0.036 2115 Dihedral : 9.522 89.235 2221 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.55 % Allowed : 12.24 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.21), residues: 1444 helix: 4.31 (0.24), residues: 339 sheet: 0.72 (0.28), residues: 336 loop : -0.75 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 222 TYR 0.009 0.001 TYR C 493 PHE 0.008 0.001 PHE C 355 TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00274 (12136) covalent geometry : angle 0.46792 (16455) SS BOND : bond 0.00125 ( 18) SS BOND : angle 0.36969 ( 36) hydrogen bonds : bond 0.05717 ( 478) hydrogen bonds : angle 4.39961 ( 1380) glycosidic custom : bond 0.00187 ( 3) glycosidic custom : angle 0.50534 ( 9) link_ALPHA1-3 : bond 0.00946 ( 3) link_ALPHA1-3 : angle 2.05367 ( 9) link_ALPHA1-6 : bond 0.00623 ( 3) link_ALPHA1-6 : angle 2.16487 ( 9) link_BETA1-4 : bond 0.00244 ( 9) link_BETA1-4 : angle 1.58439 ( 27) link_NAG-ASN : bond 0.00083 ( 9) link_NAG-ASN : angle 1.04988 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.487 Fit side-chains REVERT: A 197 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7668 (m-80) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.7230 time to fit residues: 55.4423 Evaluate side-chains 73 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.066426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.049335 restraints weight = 23413.997| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.68 r_work: 0.2435 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12181 Z= 0.097 Angle : 0.468 7.641 16572 Z= 0.238 Chirality : 0.041 0.215 1886 Planarity : 0.003 0.035 2115 Dihedral : 8.896 86.301 2221 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.55 % Allowed : 12.40 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.22), residues: 1444 helix: 4.47 (0.24), residues: 338 sheet: 0.67 (0.28), residues: 332 loop : -0.64 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.010 0.001 TYR C 493 PHE 0.007 0.001 PHE A 259 TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00212 (12136) covalent geometry : angle 0.45911 (16455) SS BOND : bond 0.00128 ( 18) SS BOND : angle 0.35127 ( 36) hydrogen bonds : bond 0.05241 ( 478) hydrogen bonds : angle 4.21533 ( 1380) glycosidic custom : bond 0.00259 ( 3) glycosidic custom : angle 0.53224 ( 9) link_ALPHA1-3 : bond 0.01008 ( 3) link_ALPHA1-3 : angle 2.07271 ( 9) link_ALPHA1-6 : bond 0.00768 ( 3) link_ALPHA1-6 : angle 2.10871 ( 9) link_BETA1-4 : bond 0.00339 ( 9) link_BETA1-4 : angle 1.45621 ( 27) link_NAG-ASN : bond 0.00131 ( 9) link_NAG-ASN : angle 0.95691 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.329 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.7572 time to fit residues: 57.7161 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.048046 restraints weight = 23403.087| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 2.62 r_work: 0.2392 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12181 Z= 0.177 Angle : 0.515 8.022 16572 Z= 0.264 Chirality : 0.043 0.216 1886 Planarity : 0.003 0.037 2115 Dihedral : 9.089 88.522 2221 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.39 % Allowed : 12.56 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1444 helix: 4.35 (0.24), residues: 336 sheet: 0.62 (0.28), residues: 340 loop : -0.76 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.007 0.001 TYR B 163 PHE 0.011 0.001 PHE C 355 TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00422 (12136) covalent geometry : angle 0.50380 (16455) SS BOND : bond 0.00143 ( 18) SS BOND : angle 0.45483 ( 36) hydrogen bonds : bond 0.06095 ( 478) hydrogen bonds : angle 4.42001 ( 1380) glycosidic custom : bond 0.00103 ( 3) glycosidic custom : angle 0.51933 ( 9) link_ALPHA1-3 : bond 0.00819 ( 3) link_ALPHA1-3 : angle 2.29948 ( 9) link_ALPHA1-6 : bond 0.00617 ( 3) link_ALPHA1-6 : angle 2.09391 ( 9) link_BETA1-4 : bond 0.00208 ( 9) link_BETA1-4 : angle 1.73728 ( 27) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 1.16024 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.492 Fit side-chains REVERT: A 197 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7715 (m-80) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.7515 time to fit residues: 56.6850 Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.065843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.048733 restraints weight = 23392.544| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.67 r_work: 0.2421 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12181 Z= 0.109 Angle : 0.482 8.099 16572 Z= 0.246 Chirality : 0.041 0.220 1886 Planarity : 0.003 0.036 2115 Dihedral : 8.771 86.612 2221 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.24 % Allowed : 12.72 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.22), residues: 1444 helix: 4.40 (0.24), residues: 338 sheet: 0.68 (0.28), residues: 330 loop : -0.68 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 222 TYR 0.008 0.001 TYR C 493 PHE 0.008 0.001 PHE C 355 TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00246 (12136) covalent geometry : angle 0.47313 (16455) SS BOND : bond 0.00121 ( 18) SS BOND : angle 0.35409 ( 36) hydrogen bonds : bond 0.05498 ( 478) hydrogen bonds : angle 4.29436 ( 1380) glycosidic custom : bond 0.00269 ( 3) glycosidic custom : angle 0.56138 ( 9) link_ALPHA1-3 : bond 0.00957 ( 3) link_ALPHA1-3 : angle 2.01618 ( 9) link_ALPHA1-6 : bond 0.00738 ( 3) link_ALPHA1-6 : angle 2.08828 ( 9) link_BETA1-4 : bond 0.00277 ( 9) link_BETA1-4 : angle 1.48075 ( 27) link_NAG-ASN : bond 0.00124 ( 9) link_NAG-ASN : angle 1.03437 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.519 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.7937 time to fit residues: 59.0208 Evaluate side-chains 69 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0030 chunk 90 optimal weight: 0.6980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.065863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.048746 restraints weight = 23579.916| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.69 r_work: 0.2419 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2302 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12181 Z= 0.110 Angle : 0.475 7.714 16572 Z= 0.242 Chirality : 0.041 0.223 1886 Planarity : 0.003 0.036 2115 Dihedral : 8.605 86.862 2221 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.16 % Allowed : 12.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.22), residues: 1444 helix: 4.56 (0.23), residues: 334 sheet: 0.69 (0.28), residues: 330 loop : -0.65 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 222 TYR 0.008 0.001 TYR C 493 PHE 0.008 0.001 PHE C 355 TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00251 (12136) covalent geometry : angle 0.46570 (16455) SS BOND : bond 0.00123 ( 18) SS BOND : angle 0.36702 ( 36) hydrogen bonds : bond 0.05445 ( 478) hydrogen bonds : angle 4.25079 ( 1380) glycosidic custom : bond 0.00226 ( 3) glycosidic custom : angle 0.52362 ( 9) link_ALPHA1-3 : bond 0.00896 ( 3) link_ALPHA1-3 : angle 2.06874 ( 9) link_ALPHA1-6 : bond 0.00738 ( 3) link_ALPHA1-6 : angle 2.08799 ( 9) link_BETA1-4 : bond 0.00287 ( 9) link_BETA1-4 : angle 1.52440 ( 27) link_NAG-ASN : bond 0.00121 ( 9) link_NAG-ASN : angle 1.01504 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5052.72 seconds wall clock time: 86 minutes 43.33 seconds (5203.33 seconds total)