Starting phenix.real_space_refine on Tue Jun 10 19:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw7_60518/06_2025/8zw7_60518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw7_60518/06_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_60518/06_2025/8zw7_60518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw7_60518/06_2025/8zw7_60518.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw7_60518/06_2025/8zw7_60518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw7_60518/06_2025/8zw7_60518.cif" } resolution = 2.09 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= 0.038 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.59, per 1000 atoms: 0.64 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: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.88 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: 4.15 Time building geometry restraints manager: 3.72 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 502 \ or resid 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 502 or resid 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 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.280 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.010 0.001 TRP B 423 HIS 0.002 0.001 HIS C 473 PHE 0.005 0.001 PHE C 355 TYR 0.011 0.001 TYR C 493 ARG 0.002 0.000 ARG A 458 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 9) link_NAG-ASN : angle 0.97524 ( 27) 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_ALPHA1-3 : bond 0.00380 ( 3) link_ALPHA1-3 : angle 1.55588 ( 9) hydrogen bonds : bond 0.17453 ( 478) hydrogen bonds : angle 6.52291 ( 1380) SS BOND : bond 0.00116 ( 18) SS BOND : angle 0.43610 ( 36) glycosidic custom : bond 0.06118 ( 3) glycosidic custom : angle 10.68582 ( 9) covalent geometry : bond 0.00305 (12136) covalent geometry : angle 0.53836 (16455) *********************** 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 : 1.319 Fit side-chains outliers start: 5 outliers final: 6 residues processed: 76 average time/residue: 1.5074 time to fit residues: 123.9682 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 : 1.420 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.0370 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 = 0.2962 r_free = 0.2962 target = 0.066160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.049244 restraints weight = 23264.211| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 2.63 r_work: 0.2424 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12181 Z= 0.114 Angle : 0.478 7.600 16572 Z= 0.247 Chirality : 0.042 0.172 1886 Planarity : 0.003 0.032 2115 Dihedral : 11.022 89.482 2231 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 (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: 1.45 (0.22), residues: 1444 helix: 4.43 (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 TRP 0.007 0.001 TRP C 423 HIS 0.003 0.001 HIS B 77 PHE 0.008 0.001 PHE B 355 TYR 0.009 0.001 TYR A 107 ARG 0.002 0.000 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 9) link_NAG-ASN : angle 0.88798 ( 27) link_ALPHA1-6 : bond 0.00355 ( 3) link_ALPHA1-6 : angle 2.31012 ( 9) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.74998 ( 27) link_ALPHA1-3 : bond 0.00840 ( 3) link_ALPHA1-3 : angle 2.47825 ( 9) hydrogen bonds : bond 0.05712 ( 478) hydrogen bonds : angle 4.95495 ( 1380) SS BOND : bond 0.00116 ( 18) SS BOND : angle 0.39347 ( 36) glycosidic custom : bond 0.00296 ( 3) glycosidic custom : angle 0.26170 ( 9) covalent geometry : bond 0.00253 (12136) covalent geometry : angle 0.46594 (16455) *********************** 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 : 1.494 Fit side-chains REVERT: A 459 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7592 (pm20) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 1.3865 time to fit residues: 115.9768 Evaluate side-chains 72 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU 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 90 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.046872 restraints weight = 23931.966| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 2.66 r_work: 0.2363 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2246 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12181 Z= 0.242 Angle : 0.551 8.082 16572 Z= 0.286 Chirality : 0.044 0.165 1886 Planarity : 0.004 0.037 2115 Dihedral : 10.797 88.148 2221 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 10.28 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.14 (0.21), residues: 1444 helix: 4.14 (0.24), residues: 336 sheet: 0.73 (0.28), residues: 330 loop : -0.83 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.006 0.001 HIS A 77 PHE 0.012 0.001 PHE C 355 TYR 0.009 0.001 TYR B 163 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 9) link_NAG-ASN : angle 1.30566 ( 27) link_ALPHA1-6 : bond 0.00369 ( 3) link_ALPHA1-6 : angle 2.19561 ( 9) link_BETA1-4 : bond 0.00184 ( 9) link_BETA1-4 : angle 2.03707 ( 27) link_ALPHA1-3 : bond 0.00820 ( 3) link_ALPHA1-3 : angle 2.32851 ( 9) hydrogen bonds : bond 0.06869 ( 478) hydrogen bonds : angle 4.82562 ( 1380) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.52814 ( 36) glycosidic custom : bond 0.00077 ( 3) glycosidic custom : angle 0.59710 ( 9) covalent geometry : bond 0.00577 (12136) covalent geometry : angle 0.53815 (16455) *********************** 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 83 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.464 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 76 average time/residue: 1.3219 time to fit residues: 109.6336 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 : 1.303 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.2933 r_free = 0.2933 target = 0.064679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.047776 restraints weight = 23492.024| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 2.64 r_work: 0.2384 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 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 : 0.004 0.028 12181 Z= 0.164 Angle : 0.497 7.256 16572 Z= 0.258 Chirality : 0.042 0.174 1886 Planarity : 0.003 0.036 2115 Dihedral : 10.378 88.771 2221 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.02 % Allowed : 11.30 % 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 (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: 1.19 (0.21), residues: 1444 helix: 4.20 (0.24), residues: 336 sheet: 0.79 (0.28), residues: 334 loop : -0.83 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.003 0.001 HIS A 77 PHE 0.010 0.001 PHE C 355 TYR 0.008 0.001 TYR C 493 ARG 0.003 0.000 ARG C 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 9) link_NAG-ASN : angle 1.13318 ( 27) link_ALPHA1-6 : bond 0.00474 ( 3) link_ALPHA1-6 : angle 2.18853 ( 9) link_BETA1-4 : bond 0.00203 ( 9) link_BETA1-4 : angle 1.79815 ( 27) link_ALPHA1-3 : bond 0.00891 ( 3) link_ALPHA1-3 : angle 2.16364 ( 9) hydrogen bonds : bond 0.06245 ( 478) hydrogen bonds : angle 4.63416 ( 1380) SS BOND : bond 0.00138 ( 18) SS BOND : angle 0.42421 ( 36) glycosidic custom : bond 0.00088 ( 3) glycosidic custom : angle 0.47705 ( 9) covalent geometry : bond 0.00387 (12136) covalent geometry : angle 0.48560 (16455) *********************** 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: 13 poor density : 70 time to evaluate : 1.466 Fit side-chains REVERT: A 197 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7690 (m-80) outliers start: 13 outliers final: 4 residues processed: 79 average time/residue: 1.4521 time to fit residues: 124.4356 Evaluate side-chains 75 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 108 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.2956 r_free = 0.2956 target = 0.065792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.048925 restraints weight = 23405.111| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.64 r_work: 0.2416 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12181 Z= 0.113 Angle : 0.467 7.361 16572 Z= 0.240 Chirality : 0.041 0.194 1886 Planarity : 0.003 0.036 2115 Dihedral : 9.763 89.455 2221 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.86 % Allowed : 11.46 % 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 (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: 1.32 (0.21), residues: 1444 helix: 4.32 (0.24), residues: 339 sheet: 0.80 (0.28), residues: 334 loop : -0.74 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS A 77 PHE 0.008 0.001 PHE C 355 TYR 0.010 0.001 TYR C 493 ARG 0.002 0.000 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 9) link_NAG-ASN : angle 0.99018 ( 27) link_ALPHA1-6 : bond 0.00613 ( 3) link_ALPHA1-6 : angle 2.17391 ( 9) link_BETA1-4 : bond 0.00266 ( 9) link_BETA1-4 : angle 1.59269 ( 27) link_ALPHA1-3 : bond 0.00992 ( 3) link_ALPHA1-3 : angle 2.08764 ( 9) hydrogen bonds : bond 0.05644 ( 478) hydrogen bonds : angle 4.41405 ( 1380) SS BOND : bond 0.00125 ( 18) SS BOND : angle 0.35790 ( 36) glycosidic custom : bond 0.00153 ( 3) glycosidic custom : angle 0.46537 ( 9) covalent geometry : bond 0.00254 (12136) covalent geometry : angle 0.45662 (16455) *********************** 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: 11 poor density : 71 time to evaluate : 1.407 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 1.3690 time to fit residues: 116.2699 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 : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 133 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.045433 restraints weight = 23969.124| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 2.71 r_work: 0.2338 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2222 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9240 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 12181 Z= 0.341 Angle : 0.616 8.994 16572 Z= 0.318 Chirality : 0.048 0.176 1886 Planarity : 0.004 0.038 2115 Dihedral : 10.301 86.851 2221 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.86 % Allowed : 11.62 % 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 (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: 0.95 (0.21), residues: 1444 helix: 3.97 (0.24), residues: 336 sheet: 0.72 (0.28), residues: 326 loop : -1.00 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.008 0.002 HIS B 20 PHE 0.013 0.001 PHE C 355 TYR 0.012 0.002 TYR B 163 ARG 0.005 0.001 ARG C 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 9) link_NAG-ASN : angle 1.49557 ( 27) link_ALPHA1-6 : bond 0.00287 ( 3) link_ALPHA1-6 : angle 2.19422 ( 9) link_BETA1-4 : bond 0.00223 ( 9) link_BETA1-4 : angle 2.24513 ( 27) link_ALPHA1-3 : bond 0.00663 ( 3) link_ALPHA1-3 : angle 2.47650 ( 9) hydrogen bonds : bond 0.07360 ( 478) hydrogen bonds : angle 4.81820 ( 1380) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.66106 ( 36) glycosidic custom : bond 0.00283 ( 3) glycosidic custom : angle 0.60381 ( 9) covalent geometry : bond 0.00823 (12136) covalent geometry : angle 0.60247 (16455) *********************** 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: 11 poor density : 66 time to evaluate : 1.410 Fit side-chains REVERT: A 197 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7852 (m-80) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 1.3777 time to fit residues: 109.2168 Evaluate side-chains 71 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 348 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.065640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.048781 restraints weight = 23503.366| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 2.65 r_work: 0.2411 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2295 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12181 Z= 0.101 Angle : 0.475 8.118 16572 Z= 0.244 Chirality : 0.041 0.195 1886 Planarity : 0.003 0.035 2115 Dihedral : 9.658 89.669 2221 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.71 % Allowed : 11.77 % 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 (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: 1.22 (0.21), residues: 1444 helix: 4.25 (0.24), residues: 339 sheet: 0.74 (0.28), residues: 334 loop : -0.82 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS B 473 PHE 0.008 0.001 PHE A 259 TYR 0.012 0.001 TYR C 493 ARG 0.002 0.000 ARG A 458 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 9) link_NAG-ASN : angle 1.05702 ( 27) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 2.12284 ( 9) link_BETA1-4 : bond 0.00287 ( 9) link_BETA1-4 : angle 1.52650 ( 27) link_ALPHA1-3 : bond 0.00969 ( 3) link_ALPHA1-3 : angle 1.91226 ( 9) hydrogen bonds : bond 0.05708 ( 478) hydrogen bonds : angle 4.45408 ( 1380) SS BOND : bond 0.00116 ( 18) SS BOND : angle 0.40942 ( 36) glycosidic custom : bond 0.00274 ( 3) glycosidic custom : angle 0.53537 ( 9) covalent geometry : bond 0.00212 (12136) covalent geometry : angle 0.46541 (16455) *********************** 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 77 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.449 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 73 average time/residue: 1.4237 time to fit residues: 113.3182 Evaluate side-chains 67 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 31 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.064471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.047542 restraints weight = 23642.178| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.65 r_work: 0.2380 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12181 Z= 0.186 Angle : 0.522 8.528 16572 Z= 0.267 Chirality : 0.043 0.197 1886 Planarity : 0.003 0.036 2115 Dihedral : 9.640 89.944 2221 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.47 % Allowed : 12.17 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.18 (0.21), residues: 1444 helix: 4.29 (0.24), residues: 336 sheet: 0.75 (0.28), residues: 332 loop : -0.87 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B 77 PHE 0.011 0.001 PHE C 355 TYR 0.008 0.001 TYR B 163 ARG 0.002 0.000 ARG C 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 9) link_NAG-ASN : angle 1.19245 ( 27) link_ALPHA1-6 : bond 0.00504 ( 3) link_ALPHA1-6 : angle 2.17105 ( 9) link_BETA1-4 : bond 0.00187 ( 9) link_BETA1-4 : angle 1.83272 ( 27) link_ALPHA1-3 : bond 0.00831 ( 3) link_ALPHA1-3 : angle 2.25743 ( 9) hydrogen bonds : bond 0.06286 ( 478) hydrogen bonds : angle 4.50860 ( 1380) SS BOND : bond 0.00151 ( 18) SS BOND : angle 0.44814 ( 36) glycosidic custom : bond 0.00071 ( 3) glycosidic custom : angle 0.47856 ( 9) covalent geometry : bond 0.00445 (12136) covalent geometry : angle 0.51021 (16455) *********************** 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 70 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.419 Fit side-chains REVERT: A 197 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7776 (m-80) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 1.4351 time to fit residues: 107.7956 Evaluate side-chains 68 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 441 LEU 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 80 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.2938 r_free = 0.2938 target = 0.064955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.048068 restraints weight = 23592.964| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 2.65 r_work: 0.2393 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12181 Z= 0.143 Angle : 0.499 8.046 16572 Z= 0.256 Chirality : 0.042 0.203 1886 Planarity : 0.003 0.036 2115 Dihedral : 9.411 89.818 2221 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.31 % Allowed : 12.32 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.21 (0.21), residues: 1444 helix: 4.32 (0.24), residues: 336 sheet: 0.73 (0.28), residues: 334 loop : -0.83 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.003 0.001 HIS B 77 PHE 0.009 0.001 PHE C 355 TYR 0.006 0.001 TYR B 488 ARG 0.002 0.000 ARG C 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 9) link_NAG-ASN : angle 1.12678 ( 27) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 2.14495 ( 9) link_BETA1-4 : bond 0.00221 ( 9) link_BETA1-4 : angle 1.68483 ( 27) link_ALPHA1-3 : bond 0.00885 ( 3) link_ALPHA1-3 : angle 2.10716 ( 9) hydrogen bonds : bond 0.05993 ( 478) hydrogen bonds : angle 4.44896 ( 1380) SS BOND : bond 0.00137 ( 18) SS BOND : angle 0.41349 ( 36) glycosidic custom : bond 0.00134 ( 3) glycosidic custom : angle 0.50828 ( 9) covalent geometry : bond 0.00336 (12136) covalent geometry : angle 0.48821 (16455) *********************** 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 68 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.358 Fit side-chains REVERT: A 197 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7701 (m-80) outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 1.5891 time to fit residues: 115.0965 Evaluate side-chains 66 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.2977 r_free = 0.2977 target = 0.066876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.050054 restraints weight = 23221.641| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 2.63 r_work: 0.2445 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2330 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12181 Z= 0.095 Angle : 0.469 7.608 16572 Z= 0.238 Chirality : 0.041 0.217 1886 Planarity : 0.003 0.035 2115 Dihedral : 8.720 86.443 2221 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.24 % Allowed : 12.64 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.40 (0.22), residues: 1444 helix: 4.52 (0.24), residues: 337 sheet: 0.72 (0.28), residues: 338 loop : -0.68 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 423 HIS 0.003 0.001 HIS B 473 PHE 0.008 0.001 PHE A 259 TYR 0.014 0.001 TYR C 493 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 9) link_NAG-ASN : angle 0.96457 ( 27) link_ALPHA1-6 : bond 0.00783 ( 3) link_ALPHA1-6 : angle 2.10604 ( 9) link_BETA1-4 : bond 0.00307 ( 9) link_BETA1-4 : angle 1.39852 ( 27) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 1.92363 ( 9) hydrogen bonds : bond 0.05175 ( 478) hydrogen bonds : angle 4.20879 ( 1380) SS BOND : bond 0.00126 ( 18) SS BOND : angle 0.36962 ( 36) glycosidic custom : bond 0.00251 ( 3) glycosidic custom : angle 0.56406 ( 9) covalent geometry : bond 0.00205 (12136) covalent geometry : angle 0.45988 (16455) ********************** 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 69 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 1.372 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 1.5617 time to fit residues: 115.0794 Evaluate side-chains 68 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.2961 r_free = 0.2961 target = 0.066204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.049056 restraints weight = 23492.478| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.68 r_work: 0.2427 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12181 Z= 0.109 Angle : 0.482 8.762 16572 Z= 0.245 Chirality : 0.041 0.222 1886 Planarity : 0.003 0.035 2115 Dihedral : 8.605 86.932 2221 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.08 % Allowed : 12.72 % 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 (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: 1.40 (0.22), residues: 1444 helix: 4.55 (0.23), residues: 336 sheet: 0.68 (0.28), residues: 340 loop : -0.67 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS B 77 PHE 0.008 0.001 PHE C 355 TYR 0.005 0.001 TYR A 107 ARG 0.001 0.000 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 0.99475 ( 27) link_ALPHA1-6 : bond 0.00736 ( 3) link_ALPHA1-6 : angle 2.10036 ( 9) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.53009 ( 27) link_ALPHA1-3 : bond 0.00911 ( 3) link_ALPHA1-3 : angle 2.12406 ( 9) hydrogen bonds : bond 0.05344 ( 478) hydrogen bonds : angle 4.20339 ( 1380) SS BOND : bond 0.00119 ( 18) SS BOND : angle 0.36727 ( 36) glycosidic custom : bond 0.00218 ( 3) glycosidic custom : angle 0.52470 ( 9) covalent geometry : bond 0.00248 (12136) covalent geometry : angle 0.47277 (16455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9618.94 seconds wall clock time: 164 minutes 15.77 seconds (9855.77 seconds total)