Starting phenix.real_space_refine on Wed May 14 15:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8r_38157/05_2025/8x8r_38157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8r_38157/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8r_38157/05_2025/8x8r_38157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8r_38157/05_2025/8x8r_38157.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8r_38157/05_2025/8x8r_38157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8r_38157/05_2025/8x8r_38157.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.76, per 1000 atoms: 0.65 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: 3.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.81 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: 3.91 Time building geometry restraints manager: 4.30 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 502 \ or resid 601)) selection = (chain 'B' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 327 or resid 337 through 502 or \ resid 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 502 or resid 601)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain '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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 30.710 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (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 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS B 186 PHE 0.010 0.001 PHE B 355 TYR 0.025 0.001 TYR C 493 ARG 0.003 0.000 ARG A 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 1.34263 ( 27) 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_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 1.69730 ( 9) hydrogen bonds : bond 0.17732 ( 467) hydrogen bonds : angle 6.67662 ( 1338) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.59095 ( 36) glycosidic custom : bond 0.06160 ( 3) glycosidic custom : angle 7.36868 ( 9) covalent geometry : bond 0.00379 (12110) covalent geometry : angle 0.70075 (16421) *********************** 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 : 1.273 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: 1.3790 time to fit residues: 162.2276 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 : 1.345 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.0050 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.7400 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.121822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091553 restraints weight = 16598.086| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.32 r_work: 0.2929 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12158 Z= 0.223 Angle : 0.622 9.847 16547 Z= 0.312 Chirality : 0.046 0.193 1889 Planarity : 0.004 0.043 2107 Dihedral : 11.821 88.404 2288 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.16 % Allowed : 10.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1436 helix: 3.21 (0.26), residues: 334 sheet: 0.16 (0.28), residues: 333 loop : -1.31 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 236 HIS 0.005 0.002 HIS A 77 PHE 0.017 0.002 PHE B 355 TYR 0.016 0.002 TYR C 493 ARG 0.003 0.000 ARG A 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 9) link_NAG-ASN : angle 1.25878 ( 27) link_ALPHA1-6 : bond 0.00395 ( 3) link_ALPHA1-6 : angle 2.53933 ( 9) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 2.19544 ( 36) link_ALPHA1-3 : bond 0.00920 ( 3) link_ALPHA1-3 : angle 1.97741 ( 9) hydrogen bonds : bond 0.06875 ( 467) hydrogen bonds : angle 5.06477 ( 1338) SS BOND : bond 0.00400 ( 18) SS BOND : angle 1.42582 ( 36) glycosidic custom : bond 0.00405 ( 3) glycosidic custom : angle 2.43363 ( 9) covalent geometry : bond 0.00548 (12110) covalent geometry : angle 0.60226 (16421) *********************** 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: 40 poor density : 101 time to evaluate : 1.292 Fit side-chains REVERT: A 37 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 455 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.6882 (ttp-170) REVERT: A 470 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7239 (pttt) REVERT: B 33 ASP cc_start: 0.8099 (m-30) cc_final: 0.7703 (m-30) REVERT: B 106 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: B 282 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 388 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5763 (pp20) REVERT: C 297 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8770 (pp30) outliers start: 40 outliers final: 11 residues processed: 126 average time/residue: 1.3950 time to fit residues: 189.5780 Evaluate side-chains 114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.123456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093388 restraints weight = 16683.463| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.33 r_work: 0.2957 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12158 Z= 0.143 Angle : 0.547 8.417 16547 Z= 0.276 Chirality : 0.043 0.195 1889 Planarity : 0.004 0.044 2107 Dihedral : 11.002 87.571 2278 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.53 % Allowed : 12.33 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1436 helix: 3.39 (0.26), residues: 336 sheet: 0.29 (0.28), residues: 323 loop : -1.18 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B 186 PHE 0.015 0.001 PHE B 355 TYR 0.014 0.001 TYR C 107 ARG 0.002 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 9) link_NAG-ASN : angle 1.12708 ( 27) link_ALPHA1-6 : bond 0.00592 ( 3) link_ALPHA1-6 : angle 2.14006 ( 9) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.99664 ( 36) link_ALPHA1-3 : bond 0.00989 ( 3) link_ALPHA1-3 : angle 1.77596 ( 9) hydrogen bonds : bond 0.06259 ( 467) hydrogen bonds : angle 4.79500 ( 1338) SS BOND : bond 0.00359 ( 18) SS BOND : angle 1.83932 ( 36) glycosidic custom : bond 0.00221 ( 3) glycosidic custom : angle 2.41996 ( 9) covalent geometry : bond 0.00334 (12110) covalent geometry : angle 0.52498 (16421) *********************** 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 134 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.389 Fit side-chains REVERT: A 266 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6746 (ptm-80) REVERT: A 383 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6791 (mp) REVERT: A 455 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7104 (ttp-170) REVERT: A 470 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7228 (pttt) REVERT: A 474 LYS cc_start: 0.7965 (tppt) cc_final: 0.7235 (tmmt) REVERT: B 33 ASP cc_start: 0.8060 (m-30) cc_final: 0.7629 (m-30) REVERT: B 64 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7452 (mtp180) REVERT: B 106 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 282 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: C 297 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8799 (pp30) outliers start: 32 outliers final: 10 residues processed: 119 average time/residue: 1.3443 time to fit residues: 172.8600 Evaluate side-chains 115 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.123003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092556 restraints weight = 16694.749| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.37 r_work: 0.2933 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12158 Z= 0.168 Angle : 0.555 8.269 16547 Z= 0.280 Chirality : 0.044 0.204 1889 Planarity : 0.004 0.043 2107 Dihedral : 10.585 84.793 2278 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.53 % Allowed : 13.83 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1436 helix: 3.40 (0.26), residues: 336 sheet: 0.32 (0.28), residues: 323 loop : -1.22 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS A 77 PHE 0.016 0.002 PHE B 355 TYR 0.018 0.002 TYR C 493 ARG 0.002 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 9) link_NAG-ASN : angle 1.18282 ( 27) link_ALPHA1-6 : bond 0.00571 ( 3) link_ALPHA1-6 : angle 2.12079 ( 9) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 1.92222 ( 36) link_ALPHA1-3 : bond 0.00991 ( 3) link_ALPHA1-3 : angle 1.86266 ( 9) hydrogen bonds : bond 0.06296 ( 467) hydrogen bonds : angle 4.65577 ( 1338) SS BOND : bond 0.00349 ( 18) SS BOND : angle 1.19465 ( 36) glycosidic custom : bond 0.00253 ( 3) glycosidic custom : angle 2.43677 ( 9) covalent geometry : bond 0.00406 (12110) covalent geometry : angle 0.53737 (16421) *********************** 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 131 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.388 Fit side-chains REVERT: A 37 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: A 266 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6799 (ptm-80) REVERT: A 398 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: A 455 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.6713 (ttp-110) REVERT: A 470 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7136 (pttt) REVERT: B 33 ASP cc_start: 0.8016 (m-30) cc_final: 0.7560 (m-30) REVERT: B 64 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7459 (mtp180) REVERT: B 106 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: B 282 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: B 388 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5760 (pp20) REVERT: B 448 LYS cc_start: 0.7422 (mtpt) cc_final: 0.7069 (mtpt) REVERT: B 464 MET cc_start: 0.8260 (mtm) cc_final: 0.7955 (mpt) REVERT: C 297 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8799 (pp30) REVERT: C 485 ASN cc_start: 0.7775 (m-40) cc_final: 0.7418 (m-40) outliers start: 32 outliers final: 11 residues processed: 117 average time/residue: 1.4731 time to fit residues: 185.5529 Evaluate side-chains 118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 106 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 297 GLN 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 128 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093556 restraints weight = 16653.311| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.37 r_work: 0.2938 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12158 Z= 0.134 Angle : 0.513 7.812 16547 Z= 0.258 Chirality : 0.043 0.214 1889 Planarity : 0.004 0.042 2107 Dihedral : 9.939 84.640 2276 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.53 % Allowed : 14.47 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1436 helix: 3.61 (0.26), residues: 336 sheet: 0.35 (0.29), residues: 323 loop : -1.15 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS C 77 PHE 0.014 0.001 PHE B 355 TYR 0.015 0.001 TYR C 107 ARG 0.002 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 9) link_NAG-ASN : angle 1.07392 ( 27) link_ALPHA1-6 : bond 0.00698 ( 3) link_ALPHA1-6 : angle 1.99232 ( 9) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 1.73462 ( 36) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 1.95030 ( 9) hydrogen bonds : bond 0.05915 ( 467) hydrogen bonds : angle 4.51416 ( 1338) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.89345 ( 36) glycosidic custom : bond 0.00408 ( 3) glycosidic custom : angle 2.56848 ( 9) covalent geometry : bond 0.00314 (12110) covalent geometry : angle 0.49741 (16421) *********************** 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 133 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.470 Fit side-chains REVERT: A 266 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6781 (ptm-80) REVERT: A 398 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: A 455 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.6673 (ttp-110) REVERT: A 470 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7019 (pttt) REVERT: B 33 ASP cc_start: 0.7961 (m-30) cc_final: 0.7480 (m-30) REVERT: B 64 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7431 (mtp180) REVERT: B 106 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 282 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: B 448 LYS cc_start: 0.7396 (mtpt) cc_final: 0.7040 (mtpt) REVERT: C 297 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8796 (pp30) REVERT: C 342 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: C 485 ASN cc_start: 0.7749 (m-40) cc_final: 0.7423 (m-40) outliers start: 32 outliers final: 13 residues processed: 117 average time/residue: 1.2663 time to fit residues: 160.9681 Evaluate side-chains 118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 383 LEU 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 A residue 475 CYS 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 B residue 441 LEU Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 342 GLU 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 139 optimal weight: 0.0030 chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 overall best weight: 1.3052 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.124397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094176 restraints weight = 16887.670| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.34 r_work: 0.2967 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12158 Z= 0.126 Angle : 0.504 7.841 16547 Z= 0.254 Chirality : 0.043 0.216 1889 Planarity : 0.003 0.041 2107 Dihedral : 9.607 85.739 2276 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.53 % Allowed : 15.34 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1436 helix: 3.69 (0.26), residues: 336 sheet: 0.37 (0.29), residues: 323 loop : -1.14 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS B 77 PHE 0.014 0.001 PHE B 355 TYR 0.019 0.001 TYR C 493 ARG 0.001 0.000 ARG A 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 9) link_NAG-ASN : angle 1.06088 ( 27) link_ALPHA1-6 : bond 0.00756 ( 3) link_ALPHA1-6 : angle 1.88133 ( 9) link_BETA1-4 : bond 0.00315 ( 12) link_BETA1-4 : angle 1.67123 ( 36) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 1.98259 ( 9) hydrogen bonds : bond 0.05761 ( 467) hydrogen bonds : angle 4.45946 ( 1338) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.78622 ( 36) glycosidic custom : bond 0.00435 ( 3) glycosidic custom : angle 2.54848 ( 9) covalent geometry : bond 0.00293 (12110) covalent geometry : angle 0.48924 (16421) *********************** 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 131 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.416 Fit side-chains REVERT: A 37 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 266 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6705 (ptm-80) REVERT: A 398 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 455 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.6642 (ttp-110) REVERT: A 470 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6973 (pttt) REVERT: B 33 ASP cc_start: 0.7928 (m-30) cc_final: 0.7421 (m-30) REVERT: B 64 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: B 85 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8121 (ptpt) REVERT: B 282 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: B 388 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5692 (pp20) REVERT: B 448 LYS cc_start: 0.7329 (mtpt) cc_final: 0.6964 (mtpt) REVERT: C 193 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: C 297 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8739 (pp30) REVERT: C 342 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: C 403 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 485 ASN cc_start: 0.7687 (m-40) cc_final: 0.7302 (m-40) outliers start: 32 outliers final: 13 residues processed: 116 average time/residue: 1.3270 time to fit residues: 166.5769 Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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 138 SER Chi-restraints excluded: chain B residue 198 VAL 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 388 GLU 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 193 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 473 HIS ** 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 = 0.3432 r_free = 0.3432 target = 0.121463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090882 restraints weight = 16854.806| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.38 r_work: 0.2917 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12158 Z= 0.247 Angle : 0.617 11.115 16547 Z= 0.310 Chirality : 0.047 0.195 1889 Planarity : 0.004 0.043 2107 Dihedral : 9.866 82.549 2276 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.85 % Allowed : 15.89 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1436 helix: 3.31 (0.26), residues: 334 sheet: 0.36 (0.29), residues: 321 loop : -1.33 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 236 HIS 0.009 0.002 HIS A 473 PHE 0.019 0.002 PHE B 355 TYR 0.019 0.002 TYR C 107 ARG 0.003 0.000 ARG C 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 9) link_NAG-ASN : angle 1.43314 ( 27) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.88830 ( 9) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 2.04403 ( 36) link_ALPHA1-3 : bond 0.00888 ( 3) link_ALPHA1-3 : angle 1.85013 ( 9) hydrogen bonds : bond 0.06857 ( 467) hydrogen bonds : angle 4.63262 ( 1338) SS BOND : bond 0.00447 ( 18) SS BOND : angle 0.91524 ( 36) glycosidic custom : bond 0.00314 ( 3) glycosidic custom : angle 2.46210 ( 9) covalent geometry : bond 0.00610 (12110) covalent geometry : angle 0.60200 (16421) *********************** 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 134 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: A 266 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6898 (ptm-80) REVERT: A 398 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: A 455 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.6763 (ttp-110) REVERT: A 470 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6967 (pttt) REVERT: B 33 ASP cc_start: 0.7980 (m-30) cc_final: 0.7660 (m-30) REVERT: B 64 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7467 (mtp180) REVERT: B 282 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: B 388 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5692 (pp20) REVERT: B 448 LYS cc_start: 0.7451 (mtpt) cc_final: 0.7075 (mtpt) REVERT: C 193 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: C 297 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8777 (pp30) REVERT: C 342 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7138 (tp30) outliers start: 36 outliers final: 13 residues processed: 118 average time/residue: 1.4440 time to fit residues: 183.6417 Evaluate side-chains 120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 388 GLU 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 194 THR Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 473 HIS ** 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 = 0.3466 r_free = 0.3466 target = 0.124006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093727 restraints weight = 16863.040| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.33 r_work: 0.2959 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12158 Z= 0.120 Angle : 0.505 8.356 16547 Z= 0.254 Chirality : 0.043 0.215 1889 Planarity : 0.004 0.041 2107 Dihedral : 9.240 85.367 2276 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.13 % Allowed : 16.76 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1436 helix: 3.57 (0.26), residues: 336 sheet: 0.34 (0.29), residues: 323 loop : -1.19 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 423 HIS 0.009 0.001 HIS A 473 PHE 0.015 0.001 PHE B 355 TYR 0.022 0.001 TYR C 493 ARG 0.002 0.000 ARG C 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 9) link_NAG-ASN : angle 1.11553 ( 27) link_ALPHA1-6 : bond 0.00809 ( 3) link_ALPHA1-6 : angle 1.79504 ( 9) link_BETA1-4 : bond 0.00295 ( 12) link_BETA1-4 : angle 1.65657 ( 36) link_ALPHA1-3 : bond 0.01080 ( 3) link_ALPHA1-3 : angle 2.00682 ( 9) hydrogen bonds : bond 0.05866 ( 467) hydrogen bonds : angle 4.48209 ( 1338) SS BOND : bond 0.00233 ( 18) SS BOND : angle 0.67647 ( 36) glycosidic custom : bond 0.00509 ( 3) glycosidic custom : angle 2.71924 ( 9) covalent geometry : bond 0.00275 (12110) covalent geometry : angle 0.49015 (16421) *********************** 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 124 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.274 Fit side-chains REVERT: A 37 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: A 266 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6684 (ptm-80) REVERT: A 398 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: A 455 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.6673 (ttp-110) REVERT: A 470 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6886 (pttt) REVERT: B 33 ASP cc_start: 0.7835 (m-30) cc_final: 0.7322 (m-30) REVERT: B 64 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: B 85 LYS cc_start: 0.8339 (ptpp) cc_final: 0.8109 (ptpt) REVERT: B 282 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: B 388 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5649 (pp20) REVERT: B 448 LYS cc_start: 0.7331 (mtpt) cc_final: 0.6965 (mtpt) REVERT: C 297 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8735 (pp30) REVERT: C 342 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: C 485 ASN cc_start: 0.7685 (m-40) cc_final: 0.7319 (m-40) outliers start: 27 outliers final: 12 residues processed: 110 average time/residue: 1.4433 time to fit residues: 170.9866 Evaluate side-chains 116 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 473 HIS ** 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 = 0.3462 r_free = 0.3462 target = 0.123162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093897 restraints weight = 16897.857| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.31 r_work: 0.2966 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12158 Z= 0.163 Angle : 0.537 8.799 16547 Z= 0.270 Chirality : 0.044 0.205 1889 Planarity : 0.004 0.042 2107 Dihedral : 9.105 85.351 2276 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1436 helix: 3.57 (0.25), residues: 334 sheet: 0.31 (0.28), residues: 323 loop : -1.23 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 423 HIS 0.009 0.001 HIS A 473 PHE 0.016 0.001 PHE B 355 TYR 0.015 0.002 TYR C 107 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 9) link_NAG-ASN : angle 1.20810 ( 27) link_ALPHA1-6 : bond 0.00776 ( 3) link_ALPHA1-6 : angle 1.82187 ( 9) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.76333 ( 36) link_ALPHA1-3 : bond 0.01016 ( 3) link_ALPHA1-3 : angle 1.95514 ( 9) hydrogen bonds : bond 0.06104 ( 467) hydrogen bonds : angle 4.47304 ( 1338) SS BOND : bond 0.00321 ( 18) SS BOND : angle 0.71515 ( 36) glycosidic custom : bond 0.00321 ( 3) glycosidic custom : angle 2.53710 ( 9) covalent geometry : bond 0.00395 (12110) covalent geometry : angle 0.52251 (16421) *********************** 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 126 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.271 Fit side-chains REVERT: A 37 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: A 266 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6861 (ptm-80) REVERT: A 398 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 455 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.6810 (ttp-110) REVERT: A 470 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7062 (pttt) REVERT: B 33 ASP cc_start: 0.7961 (m-30) cc_final: 0.7486 (m-30) REVERT: B 64 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: B 282 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: B 388 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5838 (pp20) REVERT: B 448 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7220 (mtpt) REVERT: C 193 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7043 (tp40) REVERT: C 297 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8905 (pp30) REVERT: C 342 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: C 485 ASN cc_start: 0.7745 (m-40) cc_final: 0.7421 (m-40) outliers start: 28 outliers final: 12 residues processed: 115 average time/residue: 1.3704 time to fit residues: 170.0392 Evaluate side-chains 121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 26 THR 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 388 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 473 HIS ** 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 = 0.3433 r_free = 0.3433 target = 0.121537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.091042 restraints weight = 16735.806| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.36 r_work: 0.2910 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12158 Z= 0.248 Angle : 0.615 10.643 16547 Z= 0.309 Chirality : 0.047 0.193 1889 Planarity : 0.004 0.042 2107 Dihedral : 9.312 82.930 2276 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.90 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1436 helix: 3.32 (0.26), residues: 334 sheet: 0.30 (0.28), residues: 321 loop : -1.35 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 236 HIS 0.012 0.002 HIS A 473 PHE 0.020 0.002 PHE B 355 TYR 0.025 0.002 TYR C 493 ARG 0.003 0.000 ARG C 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 9) link_NAG-ASN : angle 1.42851 ( 27) link_ALPHA1-6 : bond 0.00731 ( 3) link_ALPHA1-6 : angle 1.87669 ( 9) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 2.04589 ( 36) link_ALPHA1-3 : bond 0.00934 ( 3) link_ALPHA1-3 : angle 1.85617 ( 9) hydrogen bonds : bond 0.06844 ( 467) hydrogen bonds : angle 4.61395 ( 1338) SS BOND : bond 0.00432 ( 18) SS BOND : angle 0.82567 ( 36) glycosidic custom : bond 0.00313 ( 3) glycosidic custom : angle 2.47729 ( 9) covalent geometry : bond 0.00611 (12110) covalent geometry : angle 0.59989 (16421) ********************** 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 123 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.363 Fit side-chains REVERT: A 37 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: A 266 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6900 (ptm-80) REVERT: A 398 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: A 455 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.6813 (ttp-110) REVERT: A 470 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7145 (pttt) REVERT: B 33 ASP cc_start: 0.7921 (m-30) cc_final: 0.7595 (m-30) REVERT: B 64 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: B 282 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: B 388 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5651 (pp20) REVERT: B 448 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7153 (mtpt) REVERT: C 193 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: C 297 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: C 342 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: C 485 ASN cc_start: 0.7669 (m-40) cc_final: 0.7294 (m-40) outliers start: 24 outliers final: 12 residues processed: 113 average time/residue: 1.4599 time to fit residues: 177.6578 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 : 1.255 ------------------------------------------------------------------------------- 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 26 THR 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 388 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 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 ** A 473 HIS ** 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 = 0.3443 r_free = 0.3443 target = 0.122346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091926 restraints weight = 16630.332| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.36 r_work: 0.2934 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12158 Z= 0.189 Angle : 0.562 8.805 16547 Z= 0.283 Chirality : 0.044 0.200 1889 Planarity : 0.004 0.042 2107 Dihedral : 9.099 83.515 2276 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.90 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1436 helix: 3.34 (0.26), residues: 336 sheet: 0.33 (0.29), residues: 320 loop : -1.32 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 236 HIS 0.012 0.001 HIS A 473 PHE 0.018 0.002 PHE B 355 TYR 0.016 0.002 TYR C 107 ARG 0.002 0.000 ARG C 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 9) link_NAG-ASN : angle 1.30291 ( 27) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 1.86461 ( 9) link_BETA1-4 : bond 0.00266 ( 12) link_BETA1-4 : angle 1.88875 ( 36) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.89023 ( 9) hydrogen bonds : bond 0.06459 ( 467) hydrogen bonds : angle 4.57013 ( 1338) SS BOND : bond 0.00346 ( 18) SS BOND : angle 0.71912 ( 36) glycosidic custom : bond 0.00326 ( 3) glycosidic custom : angle 2.58664 ( 9) covalent geometry : bond 0.00462 (12110) covalent geometry : angle 0.54706 (16421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.53 seconds wall clock time: 123 minutes 10.09 seconds (7390.09 seconds total)