Starting phenix.real_space_refine on Sat Oct 11 05:12:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8r_38157/10_2025/8x8r_38157.map" } resolution = 2.84 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= 0.079 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 7371 2.51 5 N 2040 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11870 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3804 Classifications: {'peptide': 482} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3816 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 3803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3803 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 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: 2.88, per 1000 atoms: 0.24 Number of scatterers: 11870 At special positions: 0 Unit cell: (85, 88.4, 147.9, 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 2040 7.00 C 7371 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 " " NAG M 1 " - " GAL M 2 " " NAG N 1 " - " GAL N 2 " " NAG O 1 " - " GAL O 2 " BETA2-6 " GAL M 2 " - " SIA M 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL N 2 " - " SIA N 3 " " GAL O 2 " - " SIA O 3 " 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: 1.16 Conformation dependent library (CDL) restraints added in 527.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 26.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.652A pdb=" N ASP A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 81 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.502A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 369 through 380 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: 4.251A pdb=" N TYR A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 5.453A 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: 3.589A pdb=" N ASP B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 80 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.803A 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 406 through 457 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 489 through 502 removed outlier: 4.589A pdb=" N TYR B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 495 " --> pdb=" O ASP B 491 " (cutoff:3.500A) removed outlier: 5.683A 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 79 removed outlier: 3.642A pdb=" N ASP C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.598A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 406 through 457 removed outlier: 3.527A 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: 4.295A pdb=" N ASP C 495 " --> pdb=" O ASP C 491 " (cutoff:3.500A) removed outlier: 5.562A 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 367 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: 6.011A pdb=" N ILE A 53 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N CYS A 279 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.684A 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: 5.997A 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: 6.567A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE A 181 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 7.843A 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: 6.567A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.028A 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: 4.955A pdb=" N CYS A 141 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.739A 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: 5.333A 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: 3.696A pdb=" N CYS A 307 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 391 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.831A pdb=" N TYR B 353 " --> pdb=" O ASP B 368 " (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: 6.052A pdb=" N ILE B 53 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS B 279 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.733A 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: 5.878A pdb=" N PHE B 89 " --> pdb=" O MET B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.628A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE B 181 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.628A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (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: 4.884A pdb=" N CYS B 141 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.691A 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 removed outlier: 5.130A pdb=" N ARG B 203 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.721A pdb=" N CYS B 307 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.199A 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 367 removed outlier: 3.601A pdb=" N HIS C 357 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 354 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 18 " --> pdb=" O GLY C 354 " (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: 6.016A pdb=" N ILE C 53 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS C 279 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.687A 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: 5.994A pdb=" N PHE C 89 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.583A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE C 181 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.583A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AD7, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.874A pdb=" N CYS C 141 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 171 removed outlier: 5.237A pdb=" N ARG C 203 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.741A pdb=" N CYS C 307 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 391 " --> pdb=" O CYS C 307 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1338 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: 1.99 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3918 1.34 - 1.46: 2534 1.46 - 1.58: 5577 1.58 - 1.69: 3 1.69 - 1.81: 78 Bond restraints: 12110 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 1.409 1.375 0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C6 GAL N 2 " pdb=" O6 GAL N 2 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 12105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 16376 4.34 - 8.69: 39 8.69 - 13.03: 0 13.03 - 17.37: 1 17.37 - 21.71: 5 Bond angle restraints: 16421 Sorted by residual: angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 129.00 -21.71 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C3 NAG O 1 " pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 107.29 129.00 -21.71 3.00e+00 1.11e-01 5.23e+01 angle pdb=" C5 GAL N 2 " pdb=" C6 GAL N 2 " pdb=" O6 GAL N 2 " ideal model delta sigma weight residual 109.08 88.71 20.37 3.00e+00 1.11e-01 4.61e+01 angle pdb=" C5 GAL O 2 " pdb=" C6 GAL O 2 " pdb=" O6 GAL O 2 " ideal model delta sigma weight residual 109.08 88.73 20.35 3.00e+00 1.11e-01 4.60e+01 angle pdb=" C5 GAL M 2 " pdb=" C6 GAL M 2 " pdb=" O6 GAL M 2 " ideal model delta sigma weight residual 109.08 89.75 19.33 3.00e+00 1.11e-01 4.15e+01 ... (remaining 16416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 7064 22.38 - 44.76: 538 44.76 - 67.14: 75 67.14 - 89.52: 46 89.52 - 111.90: 13 Dihedral angle restraints: 7736 sinusoidal: 3566 harmonic: 4170 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 288.71 176.81 111.90 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C3 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 47.62 -62.66 110.28 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.55 110.16 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 1886 0.327 - 0.655: 0 0.655 - 0.982: 1 0.982 - 1.309: 0 1.309 - 1.636: 2 Chirality restraints: 1889 Sorted by residual: chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.89 -1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" C4 NAG O 1 " pdb=" C3 NAG O 1 " pdb=" C5 NAG O 1 " pdb=" O4 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.90 -1.64 2.00e-01 2.50e+01 6.69e+01 chirality pdb=" C2 SIA O 3 " pdb=" O6 GAL O 2 " pdb=" C1 SIA O 3 " pdb=" O6 SIA O 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.64 0.14 2.00e-02 2.50e+03 4.75e+01 ... (remaining 1886 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 144 " 0.036 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO B 145 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 75 " -0.029 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO B 76 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 75 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO C 76 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.021 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1437 2.75 - 3.29: 10229 3.29 - 3.83: 19276 3.83 - 4.36: 22676 4.36 - 4.90: 40324 Nonbonded interactions: 93942 Sorted by model distance: nonbonded pdb=" OG SER B 188 " pdb=" OE1 GLU B 192 " model vdw 2.216 3.040 nonbonded pdb=" O5 GAL O 2 " pdb=" O6 GAL O 2 " model vdw 2.219 2.432 nonbonded pdb=" O5 GAL N 2 " pdb=" O6 GAL N 2 " model vdw 2.220 2.432 nonbonded pdb=" OG1 THR A 285 " pdb=" O GLY A 288 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS C 382 " pdb=" OE1 GLU C 434 " model vdw 2.254 3.120 ... (remaining 93937 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 327 or resid 337 through 601)) selection = (chain 'C' and (resid 12 through 462 or (resid 463 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 464 through 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 'M' selection = chain 'N' selection = chain 'O' } 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: 2.510 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.004 0.062 12158 Z= 0.187 Angle : 0.858 36.087 16547 Z= 0.350 Chirality : 0.073 1.636 1889 Planarity : 0.003 0.055 2107 Dihedral : 17.007 111.901 5002 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.71 % Allowed : 11.78 % Favored : 87.51 % 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: 0.23 (0.21), residues: 1436 helix: 3.20 (0.26), residues: 335 sheet: 0.02 (0.28), residues: 318 loop : -1.22 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.025 0.001 TYR C 493 PHE 0.010 0.001 PHE B 355 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00379 (12110) covalent geometry : angle 0.70075 (16421) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.59095 ( 36) hydrogen bonds : bond 0.17732 ( 467) hydrogen bonds : angle 6.67662 ( 1338) glycosidic custom : bond 0.06160 ( 3) glycosidic custom : angle 7.36868 ( 9) link_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 1.69730 ( 9) link_ALPHA1-6 : bond 0.00372 ( 3) link_ALPHA1-6 : angle 1.58217 ( 9) link_BETA1-4 : bond 0.01761 ( 12) link_BETA1-4 : angle 9.87715 ( 36) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 1.34263 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.461 Fit side-chains REVERT: A 266 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6546 (ptm-80) REVERT: B 33 ASP cc_start: 0.7933 (m-30) cc_final: 0.7582 (m-30) REVERT: B 458 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7204 (ttt180) outliers start: 9 outliers final: 6 residues processed: 109 average time/residue: 0.6695 time to fit residues: 78.4436 Evaluate side-chains 102 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 383 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091929 restraints weight = 16629.716| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.32 r_work: 0.2945 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12158 Z= 0.197 Angle : 0.598 9.239 16547 Z= 0.300 Chirality : 0.045 0.207 1889 Planarity : 0.004 0.042 2107 Dihedral : 11.728 88.664 2288 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.08 % Allowed : 10.20 % Favored : 86.72 % 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: 0.30 (0.21), residues: 1436 helix: 3.28 (0.26), residues: 334 sheet: 0.16 (0.28), residues: 333 loop : -1.26 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.016 0.002 TYR C 493 PHE 0.016 0.002 PHE B 355 TRP 0.008 0.001 TRP C 236 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00478 (12110) covalent geometry : angle 0.57849 (16421) SS BOND : bond 0.00509 ( 18) SS BOND : angle 1.34471 ( 36) hydrogen bonds : bond 0.06688 ( 467) hydrogen bonds : angle 5.04411 ( 1338) glycosidic custom : bond 0.00638 ( 3) glycosidic custom : angle 2.65067 ( 9) link_ALPHA1-3 : bond 0.01159 ( 3) link_ALPHA1-3 : angle 2.03671 ( 9) link_ALPHA1-6 : bond 0.00537 ( 3) link_ALPHA1-6 : angle 2.43138 ( 9) link_BETA1-4 : bond 0.00590 ( 12) link_BETA1-4 : angle 2.12433 ( 36) link_NAG-ASN : bond 0.00295 ( 9) link_NAG-ASN : angle 1.18786 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.505 Fit side-chains REVERT: A 37 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: A 455 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.6874 (ttp-170) REVERT: A 470 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7235 (pttt) REVERT: B 33 ASP cc_start: 0.8075 (m-30) cc_final: 0.7675 (m-30) REVERT: B 106 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: B 282 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 388 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: C 297 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8763 (pp30) outliers start: 39 outliers final: 11 residues processed: 126 average time/residue: 0.6959 time to fit residues: 94.1400 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 456 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092690 restraints weight = 16844.987| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.38 r_work: 0.2931 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12158 Z= 0.165 Angle : 0.556 7.844 16547 Z= 0.281 Chirality : 0.044 0.196 1889 Planarity : 0.004 0.044 2107 Dihedral : 10.961 86.520 2278 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.69 % Allowed : 12.65 % Favored : 84.66 % 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: 0.42 (0.21), residues: 1436 helix: 3.34 (0.26), residues: 336 sheet: 0.29 (0.28), residues: 323 loop : -1.20 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.015 0.002 TYR C 107 PHE 0.015 0.001 PHE B 355 TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00398 (12110) covalent geometry : angle 0.53665 (16421) SS BOND : bond 0.00543 ( 18) SS BOND : angle 1.58574 ( 36) hydrogen bonds : bond 0.06409 ( 467) hydrogen bonds : angle 4.77172 ( 1338) glycosidic custom : bond 0.00202 ( 3) glycosidic custom : angle 2.31909 ( 9) link_ALPHA1-3 : bond 0.00987 ( 3) link_ALPHA1-3 : angle 1.74320 ( 9) link_ALPHA1-6 : bond 0.00560 ( 3) link_ALPHA1-6 : angle 2.08645 ( 9) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 2.01732 ( 36) link_NAG-ASN : bond 0.00183 ( 9) link_NAG-ASN : angle 1.18599 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.398 Fit side-chains REVERT: A 266 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6768 (ptm-80) REVERT: A 383 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 455 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7126 (ttp-170) REVERT: A 470 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7202 (pttt) REVERT: B 33 ASP cc_start: 0.8063 (m-30) cc_final: 0.7617 (m-30) REVERT: B 64 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7439 (mtp180) REVERT: B 106 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: B 282 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: C 297 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8792 (pp30) outliers start: 34 outliers final: 12 residues processed: 121 average time/residue: 0.7092 time to fit residues: 92.1105 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 4.9990 chunk 25 optimal weight: 0.0870 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.091336 restraints weight = 16758.930| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.37 r_work: 0.2926 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12158 Z= 0.223 Angle : 0.604 9.956 16547 Z= 0.305 Chirality : 0.046 0.198 1889 Planarity : 0.004 0.045 2107 Dihedral : 10.712 83.038 2278 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.85 % Allowed : 14.23 % Favored : 82.92 % 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: 0.26 (0.21), residues: 1436 helix: 3.23 (0.26), residues: 334 sheet: 0.28 (0.28), residues: 323 loop : -1.33 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.017 0.002 TYR C 493 PHE 0.019 0.002 PHE B 355 TRP 0.008 0.001 TRP C 423 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00550 (12110) covalent geometry : angle 0.58726 (16421) SS BOND : bond 0.00416 ( 18) SS BOND : angle 1.20997 ( 36) hydrogen bonds : bond 0.06773 ( 467) hydrogen bonds : angle 4.72617 ( 1338) glycosidic custom : bond 0.00328 ( 3) glycosidic custom : angle 2.43518 ( 9) link_ALPHA1-3 : bond 0.00899 ( 3) link_ALPHA1-3 : angle 1.84275 ( 9) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 2.15489 ( 9) link_BETA1-4 : bond 0.00288 ( 12) link_BETA1-4 : angle 2.05887 ( 36) link_NAG-ASN : bond 0.00306 ( 9) link_NAG-ASN : angle 1.35945 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.486 Fit side-chains REVERT: A 37 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: A 266 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6794 (ptm-80) REVERT: A 398 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: A 455 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.6733 (ttp-110) REVERT: A 470 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7026 (pttt) REVERT: B 33 ASP cc_start: 0.7963 (m-30) cc_final: 0.7496 (m-30) REVERT: B 64 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: B 282 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 448 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7073 (mtpt) REVERT: B 458 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7610 (ttt180) REVERT: C 212 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: C 297 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8744 (pp30) outliers start: 36 outliers final: 14 residues processed: 116 average time/residue: 0.7472 time to fit residues: 92.8540 Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 456 GLN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091636 restraints weight = 16902.777| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.39 r_work: 0.2927 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12158 Z= 0.201 Angle : 0.579 8.903 16547 Z= 0.292 Chirality : 0.045 0.201 1889 Planarity : 0.004 0.044 2107 Dihedral : 10.333 81.674 2276 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.24 % Allowed : 14.39 % Favored : 82.37 % 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: 0.30 (0.21), residues: 1436 helix: 3.28 (0.26), residues: 336 sheet: 0.28 (0.29), residues: 323 loop : -1.32 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 152 TYR 0.015 0.002 TYR C 107 PHE 0.018 0.002 PHE B 355 TRP 0.009 0.001 TRP C 423 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00493 (12110) covalent geometry : angle 0.56290 (16421) SS BOND : bond 0.00384 ( 18) SS BOND : angle 0.95060 ( 36) hydrogen bonds : bond 0.06617 ( 467) hydrogen bonds : angle 4.65074 ( 1338) glycosidic custom : bond 0.00322 ( 3) glycosidic custom : angle 2.52525 ( 9) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.85941 ( 9) link_ALPHA1-6 : bond 0.00612 ( 3) link_ALPHA1-6 : angle 2.00961 ( 9) link_BETA1-4 : bond 0.00278 ( 12) link_BETA1-4 : angle 1.95883 ( 36) link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 1.31923 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.734 Fit side-chains REVERT: A 37 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: A 266 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6832 (ptm-80) REVERT: A 398 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: A 455 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.6765 (ttp-110) REVERT: A 470 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6942 (pttt) REVERT: B 33 ASP cc_start: 0.7930 (m-30) cc_final: 0.7617 (m-30) REVERT: B 64 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7433 (mtp180) REVERT: B 282 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: B 448 LYS cc_start: 0.7413 (mtpt) cc_final: 0.7067 (mtpt) REVERT: C 297 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8781 (pp30) REVERT: C 455 ARG cc_start: 0.7330 (ttm170) cc_final: 0.7114 (ttp80) REVERT: C 485 ASN cc_start: 0.7711 (m-40) cc_final: 0.7326 (m-40) outliers start: 41 outliers final: 17 residues processed: 117 average time/residue: 0.7091 time to fit residues: 89.0742 Evaluate side-chains 122 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 224 TRP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN B 456 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094023 restraints weight = 16834.329| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.38 r_work: 0.2961 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.002 0.030 12158 Z= 0.112 Angle : 0.501 7.858 16547 Z= 0.253 Chirality : 0.042 0.217 1889 Planarity : 0.003 0.042 2107 Dihedral : 9.651 85.197 2276 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.82 % Allowed : 16.28 % Favored : 81.90 % 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: 0.56 (0.22), residues: 1436 helix: 3.62 (0.26), residues: 336 sheet: 0.33 (0.29), residues: 323 loop : -1.17 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.014 0.001 TYR C 107 PHE 0.014 0.001 PHE B 355 TRP 0.010 0.001 TRP C 423 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00248 (12110) covalent geometry : angle 0.48504 (16421) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.78152 ( 36) hydrogen bonds : bond 0.05776 ( 467) hydrogen bonds : angle 4.50581 ( 1338) glycosidic custom : bond 0.00517 ( 3) glycosidic custom : angle 2.68173 ( 9) link_ALPHA1-3 : bond 0.01075 ( 3) link_ALPHA1-3 : angle 2.01557 ( 9) link_ALPHA1-6 : bond 0.00753 ( 3) link_ALPHA1-6 : angle 1.88415 ( 9) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 1.66753 ( 36) link_NAG-ASN : bond 0.00120 ( 9) link_NAG-ASN : angle 1.05408 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.524 Fit side-chains REVERT: A 266 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6727 (ptm-80) REVERT: A 455 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.6676 (ttp-110) REVERT: A 470 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6868 (pttt) REVERT: B 33 ASP cc_start: 0.7917 (m-30) cc_final: 0.7400 (m-30) REVERT: B 64 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7389 (mtp180) REVERT: B 282 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 448 LYS cc_start: 0.7378 (mtpt) cc_final: 0.7020 (mtpt) REVERT: C 297 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8782 (pp30) REVERT: C 485 ASN cc_start: 0.7715 (m-40) cc_final: 0.7368 (m-40) outliers start: 23 outliers final: 10 residues processed: 113 average time/residue: 0.6889 time to fit residues: 83.9460 Evaluate side-chains 112 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 224 TRP Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090813 restraints weight = 16822.505| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.37 r_work: 0.2916 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12158 Z= 0.260 Angle : 0.627 11.012 16547 Z= 0.315 Chirality : 0.047 0.195 1889 Planarity : 0.004 0.044 2107 Dihedral : 9.939 82.487 2276 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.37 % Allowed : 16.60 % Favored : 81.03 % 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: 0.30 (0.21), residues: 1436 helix: 3.30 (0.26), residues: 334 sheet: 0.32 (0.29), residues: 320 loop : -1.34 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 455 TYR 0.019 0.002 TYR C 107 PHE 0.020 0.002 PHE B 355 TRP 0.008 0.001 TRP C 236 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00643 (12110) covalent geometry : angle 0.61202 (16421) SS BOND : bond 0.00459 ( 18) SS BOND : angle 0.89119 ( 36) hydrogen bonds : bond 0.06914 ( 467) hydrogen bonds : angle 4.63674 ( 1338) glycosidic custom : bond 0.00312 ( 3) glycosidic custom : angle 2.44026 ( 9) link_ALPHA1-3 : bond 0.00892 ( 3) link_ALPHA1-3 : angle 1.85916 ( 9) link_ALPHA1-6 : bond 0.00665 ( 3) link_ALPHA1-6 : angle 1.90540 ( 9) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 2.08403 ( 36) link_NAG-ASN : bond 0.00387 ( 9) link_NAG-ASN : angle 1.43751 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.485 Fit side-chains REVERT: A 37 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: A 266 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6873 (ptm-80) REVERT: A 398 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 455 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.6762 (ttp-110) REVERT: A 470 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6951 (pttt) REVERT: B 33 ASP cc_start: 0.7959 (m-30) cc_final: 0.7637 (m-30) REVERT: B 64 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 85 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8222 (ptpt) REVERT: B 282 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: B 448 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7174 (mtpt) REVERT: C 193 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7075 (tp40) REVERT: C 297 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8767 (pp30) REVERT: C 485 ASN cc_start: 0.7638 (m-40) cc_final: 0.7295 (m-40) outliers start: 30 outliers final: 13 residues processed: 117 average time/residue: 0.7395 time to fit residues: 92.6990 Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 479 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093114 restraints weight = 16647.784| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.37 r_work: 0.2951 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12158 Z= 0.131 Angle : 0.516 8.495 16547 Z= 0.260 Chirality : 0.043 0.213 1889 Planarity : 0.004 0.042 2107 Dihedral : 9.366 84.861 2276 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.90 % Allowed : 17.08 % Favored : 81.03 % 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: 0.47 (0.22), residues: 1436 helix: 3.51 (0.26), residues: 336 sheet: 0.30 (0.29), residues: 322 loop : -1.21 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 494 TYR 0.022 0.001 TYR C 493 PHE 0.015 0.001 PHE B 355 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00304 (12110) covalent geometry : angle 0.50036 (16421) SS BOND : bond 0.00273 ( 18) SS BOND : angle 0.70770 ( 36) hydrogen bonds : bond 0.06008 ( 467) hydrogen bonds : angle 4.51400 ( 1338) glycosidic custom : bond 0.00478 ( 3) glycosidic custom : angle 2.71621 ( 9) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 1.97814 ( 9) link_ALPHA1-6 : bond 0.00789 ( 3) link_ALPHA1-6 : angle 1.80117 ( 9) link_BETA1-4 : bond 0.00294 ( 12) link_BETA1-4 : angle 1.71417 ( 36) link_NAG-ASN : bond 0.00137 ( 9) link_NAG-ASN : angle 1.15939 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.483 Fit side-chains REVERT: A 37 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: A 266 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6714 (ptm-80) REVERT: A 398 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 455 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.6743 (ttp-110) REVERT: A 470 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6899 (pttt) REVERT: B 33 ASP cc_start: 0.7869 (m-30) cc_final: 0.7345 (m-30) REVERT: B 64 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: B 85 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8151 (ptpt) REVERT: B 282 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 448 LYS cc_start: 0.7363 (mtpt) cc_final: 0.7007 (mtpt) REVERT: C 193 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.6922 (tp40) REVERT: C 297 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8769 (pp30) REVERT: C 342 GLU cc_start: 0.7868 (tt0) cc_final: 0.7174 (tp30) REVERT: C 485 ASN cc_start: 0.7672 (m-40) cc_final: 0.7305 (m-40) outliers start: 24 outliers final: 11 residues processed: 114 average time/residue: 0.7197 time to fit residues: 88.0197 Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 224 TRP Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 449 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092017 restraints weight = 16669.520| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.36 r_work: 0.2914 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12158 Z= 0.190 Angle : 0.560 9.011 16547 Z= 0.282 Chirality : 0.045 0.203 1889 Planarity : 0.004 0.043 2107 Dihedral : 9.305 84.388 2276 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 16.76 % Favored : 80.95 % 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: 0.39 (0.22), residues: 1436 helix: 3.48 (0.26), residues: 334 sheet: 0.29 (0.29), residues: 322 loop : -1.28 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 203 TYR 0.023 0.002 TYR C 493 PHE 0.017 0.002 PHE B 355 TRP 0.008 0.001 TRP C 423 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00464 (12110) covalent geometry : angle 0.54517 (16421) SS BOND : bond 0.00338 ( 18) SS BOND : angle 0.75583 ( 36) hydrogen bonds : bond 0.06377 ( 467) hydrogen bonds : angle 4.53227 ( 1338) glycosidic custom : bond 0.00353 ( 3) glycosidic custom : angle 2.53663 ( 9) link_ALPHA1-3 : bond 0.01023 ( 3) link_ALPHA1-3 : angle 1.93575 ( 9) link_ALPHA1-6 : bond 0.00762 ( 3) link_ALPHA1-6 : angle 1.83858 ( 9) link_BETA1-4 : bond 0.00278 ( 12) link_BETA1-4 : angle 1.86471 ( 36) link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 1.28156 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.473 Fit side-chains REVERT: A 37 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: A 266 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6829 (ptm-80) REVERT: A 398 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: A 455 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.6733 (ttp-110) REVERT: A 470 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6881 (pttt) REVERT: B 33 ASP cc_start: 0.7915 (m-30) cc_final: 0.7392 (m-30) REVERT: B 64 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: B 282 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 448 LYS cc_start: 0.7390 (mtpt) cc_final: 0.7096 (mtpt) REVERT: C 193 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: C 297 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8781 (pp30) REVERT: C 342 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: C 485 ASN cc_start: 0.7680 (m-40) cc_final: 0.7320 (m-40) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 0.6670 time to fit residues: 84.0897 Evaluate side-chains 120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 479 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096187 restraints weight = 16878.580| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.35 r_work: 0.2989 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12158 Z= 0.108 Angle : 0.491 8.053 16547 Z= 0.247 Chirality : 0.042 0.219 1889 Planarity : 0.003 0.042 2107 Dihedral : 8.761 87.124 2276 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.66 % Allowed : 17.39 % Favored : 80.95 % 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: 0.60 (0.22), residues: 1436 helix: 3.70 (0.25), residues: 336 sheet: 0.33 (0.29), residues: 322 loop : -1.14 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.014 0.001 TYR A 107 PHE 0.013 0.001 PHE B 355 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00241 (12110) covalent geometry : angle 0.47617 (16421) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.65250 ( 36) hydrogen bonds : bond 0.05601 ( 467) hydrogen bonds : angle 4.40715 ( 1338) glycosidic custom : bond 0.00556 ( 3) glycosidic custom : angle 2.73744 ( 9) link_ALPHA1-3 : bond 0.01093 ( 3) link_ALPHA1-3 : angle 1.97432 ( 9) link_ALPHA1-6 : bond 0.00866 ( 3) link_ALPHA1-6 : angle 1.82417 ( 9) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.58435 ( 36) link_NAG-ASN : bond 0.00135 ( 9) link_NAG-ASN : angle 1.05807 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.490 Fit side-chains REVERT: A 37 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 266 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6824 (ptm-80) REVERT: A 455 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.6760 (ttp-110) REVERT: A 470 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7034 (pttt) REVERT: B 33 ASP cc_start: 0.7919 (m-30) cc_final: 0.7443 (m-30) REVERT: B 64 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: B 282 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 448 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7233 (mtpt) REVERT: C 174 TYR cc_start: 0.9029 (m-80) cc_final: 0.8774 (m-80) REVERT: C 297 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8935 (pp30) REVERT: C 342 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: C 403 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: C 485 ASN cc_start: 0.7762 (m-40) cc_final: 0.7485 (m-40) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.6990 time to fit residues: 82.8140 Evaluate side-chains 114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 224 TRP Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098870 restraints weight = 16762.975| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.33 r_work: 0.3017 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12158 Z= 0.092 Angle : 0.460 8.112 16547 Z= 0.231 Chirality : 0.041 0.213 1889 Planarity : 0.003 0.041 2107 Dihedral : 8.137 89.392 2276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.19 % Allowed : 17.94 % Favored : 80.87 % 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: 0.85 (0.22), residues: 1436 helix: 4.12 (0.25), residues: 334 sheet: 0.47 (0.30), residues: 310 loop : -1.05 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.030 0.001 TYR C 493 PHE 0.011 0.001 PHE B 355 TRP 0.010 0.001 TRP C 423 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00195 (12110) covalent geometry : angle 0.44552 (16421) SS BOND : bond 0.00181 ( 18) SS BOND : angle 0.61071 ( 36) hydrogen bonds : bond 0.04920 ( 467) hydrogen bonds : angle 4.19920 ( 1338) glycosidic custom : bond 0.00676 ( 3) glycosidic custom : angle 2.59948 ( 9) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.90708 ( 9) link_ALPHA1-6 : bond 0.00954 ( 3) link_ALPHA1-6 : angle 1.90341 ( 9) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.45106 ( 36) link_NAG-ASN : bond 0.00193 ( 9) link_NAG-ASN : angle 0.92134 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.12 seconds wall clock time: 63 minutes 45.22 seconds (3825.22 seconds total)