Starting phenix.real_space_refine on Sat Aug 23 11:42:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw5_60516/08_2025/8zw5_60516.map" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 7347 2.51 5 N 2037 2.21 5 O 2387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11828 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: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.12, per 1000 atoms: 0.26 Number of scatterers: 11828 At special positions: 0 Unit cell: (86.7, 85.85, 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 2387 8.00 N 2037 7.00 C 7347 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=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 479 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " BETA2-3 " GAL J 1 " - " SIA J 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL K 1 " - " SIA K 2 " " GAL L 1 " - " SIA L 2 " NAG-ASN " NAG A 601 " - " ASN A 40 " " NAG B 601 " - " ASN B 40 " " NAG C 601 " - " ASN C 40 " " NAG D 1 " - " ASN A 167 " " NAG E 1 " - " ASN A 287 " " NAG F 1 " - " ASN B 167 " " NAG G 1 " - " ASN B 287 " " NAG H 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 287 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 531.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 27.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 82 removed outlier: 5.317A pdb=" N VAL A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 406 through 457 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 493 through 502 removed outlier: 3.529A pdb=" N PHE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 75 through 82 removed outlier: 5.187A pdb=" N VAL B 80 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 82 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.501A pdb=" N LEU B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 406 through 457 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 493 through 502 removed outlier: 3.977A pdb=" N PHE B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 75 through 82 removed outlier: 5.237A pdb=" N VAL C 80 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.515A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.559A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.534A pdb=" N VAL C 386 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 457 Processing helix chain 'C' and resid 476 through 486 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 493 through 502 removed outlier: 3.660A pdb=" N PHE C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 368 removed outlier: 4.823A pdb=" N TYR A 353 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 56 removed outlier: 5.852A pdb=" N ILE A 53 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS A 279 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 55 " --> pdb=" O CYS A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.807A pdb=" N LEU A 61 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 102 through 103 removed outlier: 5.159A pdb=" N ILE A 181 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 258 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 103 removed outlier: 8.026A pdb=" N ILE A 181 " --> pdb=" O PRO A 256 " (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: 4.909A pdb=" N CYS A 141 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.744A 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: 5.339A 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 290 removed outlier: 4.188A pdb=" N CYS A 283 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 307 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 391 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 364 through 368 removed outlier: 4.778A 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: 5.891A pdb=" N ILE B 53 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS B 279 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 55 " --> pdb=" O CYS B 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.756A pdb=" N LEU B 61 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE B 89 " --> pdb=" O MET B 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 103 removed outlier: 5.171A pdb=" N ILE B 181 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 258 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 102 through 103 removed outlier: 8.002A pdb=" N ILE B 181 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AC4, first strand: chain 'B' and resid 138 through 143 removed outlier: 4.878A pdb=" N CYS B 141 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.709A 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: 4.884A 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 290 removed outlier: 4.190A pdb=" N CYS B 283 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 307 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN B 391 " --> pdb=" O CYS B 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 364 through 367 Processing sheet with id=AC8, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AD1, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'C' and resid 53 through 56 removed outlier: 5.860A pdb=" N ILE C 53 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N CYS C 279 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 55 " --> pdb=" O CYS C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.791A pdb=" N LEU C 61 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 102 through 103 removed outlier: 5.188A pdb=" N ILE C 181 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 258 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 102 through 103 removed outlier: 8.015A pdb=" N ILE C 181 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AD7, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.871A pdb=" N CYS C 141 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 146 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 171 removed outlier: 4.973A 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 290 removed outlier: 4.220A pdb=" N CYS C 283 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS C 307 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN C 391 " --> pdb=" O CYS C 307 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.58 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: 3911 1.34 - 1.46: 2871 1.46 - 1.58: 5205 1.58 - 1.71: 3 1.71 - 1.83: 78 Bond restraints: 12068 Sorted by residual: bond pdb=" C5 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C5 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 16083 2.03 - 4.07: 235 4.07 - 6.10: 34 6.10 - 8.14: 10 8.14 - 10.17: 2 Bond angle restraints: 16364 Sorted by residual: angle pdb=" CA LEU B 113 " pdb=" CB LEU B 113 " pdb=" CG LEU B 113 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.45e+00 angle pdb=" CA LEU C 113 " pdb=" CB LEU C 113 " pdb=" CG LEU C 113 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.83e+00 angle pdb=" CB ASN B 167 " pdb=" CG ASN B 167 " pdb=" ND2 ASN B 167 " ideal model delta sigma weight residual 116.40 120.01 -3.61 1.50e+00 4.44e-01 5.79e+00 angle pdb=" CA LEU C 441 " pdb=" CB LEU C 441 " pdb=" CG LEU C 441 " ideal model delta sigma weight residual 116.30 124.05 -7.75 3.50e+00 8.16e-02 4.90e+00 angle pdb=" CA LEU A 441 " pdb=" CB LEU A 441 " pdb=" CG LEU A 441 " ideal model delta sigma weight residual 116.30 123.95 -7.65 3.50e+00 8.16e-02 4.78e+00 ... (remaining 16359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 6960 22.08 - 44.17: 560 44.17 - 66.25: 95 66.25 - 88.34: 46 88.34 - 110.42: 12 Dihedral angle restraints: 7673 sinusoidal: 3503 harmonic: 4170 Sorted by residual: dihedral pdb=" CA TRP B 86 " pdb=" C TRP B 86 " pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TRP C 86 " pdb=" C TRP C 86 " pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.29 110.42 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 7670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 1870 0.248 - 0.497: 3 0.497 - 0.745: 0 0.745 - 0.994: 0 0.994 - 1.242: 1 Chirality restraints: 1874 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 167 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.86e+01 chirality pdb=" C2 SIA K 2 " pdb=" O3 GAL K 1 " pdb=" C1 SIA K 2 " pdb=" O6 SIA K 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.44 -0.06 2.00e-02 2.50e+03 9.60e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1871 not shown) Planarity restraints: 2113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 167 " 0.002 2.00e-02 2.50e+03 1.36e-02 2.30e+00 pdb=" CG ASN B 167 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 167 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 167 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 75 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO B 76 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 294 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 295 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.017 5.00e-02 4.00e+02 ... (remaining 2110 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 777 2.74 - 3.28: 10643 3.28 - 3.82: 19722 3.82 - 4.36: 23503 4.36 - 4.90: 39700 Nonbonded interactions: 94345 Sorted by model distance: nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 472 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASN B 167 " pdb=" ND2 ASN B 248 " model vdw 2.238 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" OD2 ASP A 463 " model vdw 2.297 3.120 nonbonded pdb=" OG SER B 138 " pdb=" O1A SIA L 2 " model vdw 2.345 3.040 nonbonded pdb=" NE2 GLN C 373 " pdb=" OD1 ASP C 377 " model vdw 2.345 3.120 ... (remaining 94340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 462 or (resid 463 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 464 through 601) \ ) selection = (chain 'B' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 327 or resid 337 through 601)) selection = (chain 'C' and (resid 12 through 462 or (resid 463 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 464 through 601)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 0.065 12113 Z= 0.180 Angle : 0.828 36.615 16481 Z= 0.357 Chirality : 0.055 1.242 1874 Planarity : 0.004 0.031 2104 Dihedral : 17.372 110.421 4939 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.71 % Allowed : 12.17 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1436 helix: 3.05 (0.26), residues: 333 sheet: 0.62 (0.28), residues: 325 loop : -1.04 (0.18), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 64 TYR 0.010 0.001 TYR C 107 PHE 0.014 0.001 PHE C 355 TRP 0.009 0.001 TRP B 423 HIS 0.008 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00343 (12068) covalent geometry : angle 0.63294 (16364) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.03490 ( 36) hydrogen bonds : bond 0.13071 ( 489) hydrogen bonds : angle 5.96532 ( 1422) link_ALPHA1-3 : bond 0.00210 ( 3) link_ALPHA1-3 : angle 1.97274 ( 9) link_ALPHA1-6 : bond 0.00350 ( 3) link_ALPHA1-6 : angle 1.52718 ( 9) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 2.36621 ( 27) link_BETA2-3 : bond 0.06467 ( 3) link_BETA2-3 : angle 20.07746 ( 9) link_NAG-ASN : bond 0.00786 ( 9) link_NAG-ASN : angle 5.63353 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: B 472 TYR cc_start: 0.7552 (m-80) cc_final: 0.7154 (m-80) REVERT: C 212 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8145 (pt0) outliers start: 9 outliers final: 5 residues processed: 140 average time/residue: 0.7788 time to fit residues: 115.7955 Evaluate side-chains 94 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 212 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** 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 = 0.3046 r_free = 0.3046 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.045635 restraints weight = 22328.850| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 2.66 r_work: 0.2323 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2206 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12113 Z= 0.217 Angle : 0.616 20.907 16481 Z= 0.306 Chirality : 0.050 0.875 1874 Planarity : 0.004 0.041 2104 Dihedral : 11.691 86.887 2227 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.45 % Allowed : 12.73 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.21), residues: 1436 helix: 3.41 (0.25), residues: 335 sheet: 0.62 (0.28), residues: 327 loop : -1.13 (0.18), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 501 TYR 0.025 0.001 TYR C 472 PHE 0.013 0.002 PHE C 355 TRP 0.009 0.001 TRP B 423 HIS 0.008 0.002 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00524 (12068) covalent geometry : angle 0.56484 (16364) SS BOND : bond 0.00290 ( 18) SS BOND : angle 1.07531 ( 36) hydrogen bonds : bond 0.07291 ( 489) hydrogen bonds : angle 4.99699 ( 1422) link_ALPHA1-3 : bond 0.00666 ( 3) link_ALPHA1-3 : angle 1.82133 ( 9) link_ALPHA1-6 : bond 0.00322 ( 3) link_ALPHA1-6 : angle 1.99047 ( 9) link_BETA1-4 : bond 0.00309 ( 9) link_BETA1-4 : angle 2.30613 ( 27) link_BETA2-3 : bond 0.00176 ( 3) link_BETA2-3 : angle 4.21377 ( 9) link_NAG-ASN : bond 0.00729 ( 9) link_NAG-ASN : angle 4.77997 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9064 (mtm) cc_final: 0.8722 (mtm) REVERT: B 212 GLN cc_start: 0.9579 (OUTLIER) cc_final: 0.9000 (pt0) REVERT: B 454 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8004 (ttp-170) REVERT: B 464 MET cc_start: 0.9103 (mtm) cc_final: 0.8871 (mtm) REVERT: C 462 GLU cc_start: 0.7291 (tt0) cc_final: 0.7010 (mt-10) REVERT: C 472 TYR cc_start: 0.8693 (m-80) cc_final: 0.8125 (m-80) REVERT: C 493 TYR cc_start: 0.9419 (m-80) cc_final: 0.9194 (m-80) outliers start: 31 outliers final: 14 residues processed: 114 average time/residue: 0.8124 time to fit residues: 98.5824 Evaluate side-chains 98 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 403 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.071632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.045253 restraints weight = 22516.383| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 2.66 r_work: 0.2317 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2200 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12113 Z= 0.217 Angle : 0.601 19.966 16481 Z= 0.299 Chirality : 0.049 0.812 1874 Planarity : 0.004 0.054 2104 Dihedral : 11.306 85.484 2222 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.90 % Allowed : 13.04 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1436 helix: 3.66 (0.25), residues: 333 sheet: 0.65 (0.28), residues: 327 loop : -1.15 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 64 TYR 0.036 0.002 TYR B 472 PHE 0.012 0.001 PHE C 355 TRP 0.008 0.001 TRP A 423 HIS 0.006 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00522 (12068) covalent geometry : angle 0.55277 (16364) SS BOND : bond 0.00288 ( 18) SS BOND : angle 0.99131 ( 36) hydrogen bonds : bond 0.07165 ( 489) hydrogen bonds : angle 4.84628 ( 1422) link_ALPHA1-3 : bond 0.00563 ( 3) link_ALPHA1-3 : angle 1.75870 ( 9) link_ALPHA1-6 : bond 0.00355 ( 3) link_ALPHA1-6 : angle 1.92909 ( 9) link_BETA1-4 : bond 0.00289 ( 9) link_BETA1-4 : angle 2.20615 ( 27) link_BETA2-3 : bond 0.00085 ( 3) link_BETA2-3 : angle 4.06739 ( 9) link_NAG-ASN : bond 0.00723 ( 9) link_NAG-ASN : angle 4.60102 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9145 (mtm) cc_final: 0.8846 (mtm) REVERT: B 212 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8911 (pt0) REVERT: B 382 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7492 (ttpp) REVERT: B 454 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8144 (ttp-170) REVERT: B 464 MET cc_start: 0.9089 (mtm) cc_final: 0.8841 (mtm) REVERT: C 212 GLN cc_start: 0.9554 (OUTLIER) cc_final: 0.8767 (pt0) REVERT: C 472 TYR cc_start: 0.8613 (m-80) cc_final: 0.8257 (m-10) outliers start: 24 outliers final: 14 residues processed: 104 average time/residue: 0.7289 time to fit residues: 81.4485 Evaluate side-chains 100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 403 GLU 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 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 473 HIS ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.046495 restraints weight = 22396.836| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 2.60 r_work: 0.2338 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12113 Z= 0.142 Angle : 0.554 18.505 16481 Z= 0.275 Chirality : 0.046 0.749 1874 Planarity : 0.003 0.037 2104 Dihedral : 10.754 80.701 2220 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.66 % Allowed : 13.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1436 helix: 3.88 (0.24), residues: 333 sheet: 0.81 (0.29), residues: 323 loop : -1.12 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.028 0.001 TYR B 472 PHE 0.012 0.001 PHE B 502 TRP 0.011 0.001 TRP C 352 HIS 0.006 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00327 (12068) covalent geometry : angle 0.50831 (16364) SS BOND : bond 0.00276 ( 18) SS BOND : angle 0.95501 ( 36) hydrogen bonds : bond 0.06564 ( 489) hydrogen bonds : angle 4.63958 ( 1422) link_ALPHA1-3 : bond 0.00706 ( 3) link_ALPHA1-3 : angle 1.73624 ( 9) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.89728 ( 9) link_BETA1-4 : bond 0.00354 ( 9) link_BETA1-4 : angle 2.06794 ( 27) link_BETA2-3 : bond 0.00050 ( 3) link_BETA2-3 : angle 3.63646 ( 9) link_NAG-ASN : bond 0.00715 ( 9) link_NAG-ASN : angle 4.28671 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9195 (mtm) cc_final: 0.8914 (mtm) REVERT: B 212 GLN cc_start: 0.9554 (OUTLIER) cc_final: 0.8860 (pt0) REVERT: B 382 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7475 (ttpp) REVERT: B 454 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8150 (ttp-170) REVERT: C 212 GLN cc_start: 0.9550 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: C 277 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8580 (mm-30) REVERT: C 462 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6931 (mt-10) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 0.7457 time to fit residues: 80.4526 Evaluate side-chains 99 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 403 GLU 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 10 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.045152 restraints weight = 22804.705| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.66 r_work: 0.2314 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2199 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12113 Z= 0.195 Angle : 0.580 19.027 16481 Z= 0.287 Chirality : 0.047 0.774 1874 Planarity : 0.003 0.038 2104 Dihedral : 10.633 80.306 2220 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 12.96 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.21), residues: 1436 helix: 3.95 (0.24), residues: 333 sheet: 0.75 (0.28), residues: 327 loop : -1.13 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.035 0.002 TYR C 472 PHE 0.011 0.001 PHE C 355 TRP 0.007 0.001 TRP A 236 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00466 (12068) covalent geometry : angle 0.53522 (16364) SS BOND : bond 0.00279 ( 18) SS BOND : angle 0.92203 ( 36) hydrogen bonds : bond 0.06788 ( 489) hydrogen bonds : angle 4.63163 ( 1422) link_ALPHA1-3 : bond 0.00633 ( 3) link_ALPHA1-3 : angle 1.80683 ( 9) link_ALPHA1-6 : bond 0.00459 ( 3) link_ALPHA1-6 : angle 1.92534 ( 9) link_BETA1-4 : bond 0.00291 ( 9) link_BETA1-4 : angle 2.10901 ( 27) link_BETA2-3 : bond 0.00100 ( 3) link_BETA2-3 : angle 3.69251 ( 9) link_NAG-ASN : bond 0.00718 ( 9) link_NAG-ASN : angle 4.40826 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9181 (mtm) cc_final: 0.8926 (mtm) REVERT: B 212 GLN cc_start: 0.9573 (OUTLIER) cc_final: 0.8878 (pt0) REVERT: B 342 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9156 (mp0) REVERT: B 382 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7495 (ttpp) REVERT: B 454 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: C 212 GLN cc_start: 0.9572 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: C 277 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8488 (mm-30) REVERT: C 472 TYR cc_start: 0.8296 (m-80) cc_final: 0.7992 (m-80) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.6363 time to fit residues: 66.1915 Evaluate side-chains 96 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 403 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 118 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 128 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.045202 restraints weight = 22701.374| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 2.65 r_work: 0.2316 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2201 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12113 Z= 0.183 Angle : 0.579 18.775 16481 Z= 0.287 Chirality : 0.047 0.760 1874 Planarity : 0.003 0.035 2104 Dihedral : 10.456 78.900 2220 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.82 % Allowed : 13.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.21), residues: 1436 helix: 3.98 (0.24), residues: 333 sheet: 0.78 (0.29), residues: 327 loop : -1.10 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.024 0.001 TYR B 472 PHE 0.015 0.001 PHE B 502 TRP 0.008 0.001 TRP A 352 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00437 (12068) covalent geometry : angle 0.53457 (16364) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.94591 ( 36) hydrogen bonds : bond 0.06738 ( 489) hydrogen bonds : angle 4.59417 ( 1422) link_ALPHA1-3 : bond 0.00642 ( 3) link_ALPHA1-3 : angle 1.83368 ( 9) link_ALPHA1-6 : bond 0.00499 ( 3) link_ALPHA1-6 : angle 1.87432 ( 9) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 2.10364 ( 27) link_BETA2-3 : bond 0.00087 ( 3) link_BETA2-3 : angle 3.63336 ( 9) link_NAG-ASN : bond 0.00720 ( 9) link_NAG-ASN : angle 4.35579 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.8855 (pt0) REVERT: B 342 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9165 (mp0) REVERT: B 358 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 382 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7512 (ttpp) REVERT: B 454 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8126 (ttp-170) REVERT: C 212 GLN cc_start: 0.9573 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: C 277 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 472 TYR cc_start: 0.8293 (m-80) cc_final: 0.7831 (m-80) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.6595 time to fit residues: 71.9822 Evaluate side-chains 97 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 501 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 350 ASP 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 136 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.046141 restraints weight = 22539.312| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 2.65 r_work: 0.2344 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2228 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12113 Z= 0.126 Angle : 0.555 17.499 16481 Z= 0.274 Chirality : 0.045 0.703 1874 Planarity : 0.003 0.034 2104 Dihedral : 10.061 76.872 2220 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.58 % Allowed : 13.99 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.21), residues: 1436 helix: 4.11 (0.24), residues: 333 sheet: 0.86 (0.29), residues: 327 loop : -1.03 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.022 0.001 TYR C 472 PHE 0.012 0.001 PHE B 502 TRP 0.008 0.001 TRP C 352 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00284 (12068) covalent geometry : angle 0.51393 (16364) SS BOND : bond 0.00199 ( 18) SS BOND : angle 0.91647 ( 36) hydrogen bonds : bond 0.06253 ( 489) hydrogen bonds : angle 4.45938 ( 1422) link_ALPHA1-3 : bond 0.00784 ( 3) link_ALPHA1-3 : angle 1.80269 ( 9) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 1.82205 ( 9) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 1.99202 ( 27) link_BETA2-3 : bond 0.00028 ( 3) link_BETA2-3 : angle 3.36085 ( 9) link_NAG-ASN : bond 0.00711 ( 9) link_NAG-ASN : angle 4.07933 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9078 (mtm) cc_final: 0.8857 (mtm) REVERT: B 212 GLN cc_start: 0.9564 (OUTLIER) cc_final: 0.8795 (pt0) REVERT: B 342 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9179 (mp0) REVERT: B 346 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 358 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 382 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7419 (ttpp) REVERT: C 277 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8486 (mm-30) REVERT: C 462 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6777 (mt-10) outliers start: 20 outliers final: 7 residues processed: 98 average time/residue: 0.6319 time to fit residues: 66.4252 Evaluate side-chains 88 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 444 SER 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 31 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.045232 restraints weight = 22559.448| |-----------------------------------------------------------------------------| r_work (start): 0.2449 rms_B_bonded: 2.65 r_work: 0.2321 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2206 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12113 Z= 0.185 Angle : 0.589 18.318 16481 Z= 0.293 Chirality : 0.047 0.742 1874 Planarity : 0.003 0.035 2104 Dihedral : 9.997 76.794 2219 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.03 % Allowed : 14.78 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.21), residues: 1436 helix: 4.09 (0.24), residues: 333 sheet: 0.83 (0.29), residues: 327 loop : -1.06 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 501 TYR 0.035 0.001 TYR C 472 PHE 0.019 0.001 PHE B 502 TRP 0.007 0.001 TRP B 236 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00441 (12068) covalent geometry : angle 0.54778 (16364) SS BOND : bond 0.00241 ( 18) SS BOND : angle 0.91569 ( 36) hydrogen bonds : bond 0.06635 ( 489) hydrogen bonds : angle 4.50759 ( 1422) link_ALPHA1-3 : bond 0.00685 ( 3) link_ALPHA1-3 : angle 1.92494 ( 9) link_ALPHA1-6 : bond 0.00546 ( 3) link_ALPHA1-6 : angle 1.85218 ( 9) link_BETA1-4 : bond 0.00282 ( 9) link_BETA1-4 : angle 2.08101 ( 27) link_BETA2-3 : bond 0.00072 ( 3) link_BETA2-3 : angle 3.53591 ( 9) link_NAG-ASN : bond 0.00733 ( 9) link_NAG-ASN : angle 4.26137 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9127 (mtm) cc_final: 0.8230 (mtm) REVERT: B 212 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.8801 (pt0) REVERT: B 342 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9213 (mp0) REVERT: B 346 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 358 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 382 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7494 (ttpp) REVERT: C 277 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8481 (mm-30) REVERT: C 464 MET cc_start: 0.8815 (mtm) cc_final: 0.8356 (mpt) REVERT: C 472 TYR cc_start: 0.8104 (m-10) cc_final: 0.7651 (m-80) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.7313 time to fit residues: 71.1817 Evaluate side-chains 89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN C 456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.046970 restraints weight = 22257.788| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 2.64 r_work: 0.2363 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12113 Z= 0.113 Angle : 0.540 16.380 16481 Z= 0.267 Chirality : 0.045 0.666 1874 Planarity : 0.003 0.034 2104 Dihedral : 9.482 75.908 2219 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.11 % Allowed : 14.70 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1436 helix: 4.30 (0.24), residues: 333 sheet: 0.94 (0.29), residues: 325 loop : -0.86 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.030 0.001 TYR C 472 PHE 0.018 0.001 PHE C 502 TRP 0.008 0.001 TRP A 423 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00250 (12068) covalent geometry : angle 0.50257 (16364) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.90686 ( 36) hydrogen bonds : bond 0.05867 ( 489) hydrogen bonds : angle 4.30842 ( 1422) link_ALPHA1-3 : bond 0.00882 ( 3) link_ALPHA1-3 : angle 1.82964 ( 9) link_ALPHA1-6 : bond 0.00734 ( 3) link_ALPHA1-6 : angle 1.88354 ( 9) link_BETA1-4 : bond 0.00396 ( 9) link_BETA1-4 : angle 1.91371 ( 27) link_BETA2-3 : bond 0.00037 ( 3) link_BETA2-3 : angle 3.09768 ( 9) link_NAG-ASN : bond 0.00675 ( 9) link_NAG-ASN : angle 3.84673 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9214 (mp0) REVERT: B 346 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 358 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 382 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7417 (ttpp) REVERT: B 388 GLU cc_start: 0.8366 (tp30) cc_final: 0.8132 (tm-30) REVERT: C 358 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 462 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6605 (mt-10) REVERT: C 464 MET cc_start: 0.8699 (mtm) cc_final: 0.8132 (mpt) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.7880 time to fit residues: 83.5504 Evaluate side-chains 93 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 191 GLN B 378 GLN C 378 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.046432 restraints weight = 22669.741| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 2.68 r_work: 0.2353 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12113 Z= 0.137 Angle : 0.558 16.737 16481 Z= 0.277 Chirality : 0.046 0.681 1874 Planarity : 0.003 0.035 2104 Dihedral : 9.339 75.704 2216 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.03 % Allowed : 15.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1436 helix: 4.29 (0.24), residues: 333 sheet: 0.94 (0.29), residues: 325 loop : -0.86 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.022 0.001 TYR C 472 PHE 0.020 0.001 PHE B 502 TRP 0.008 0.001 TRP A 423 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00320 (12068) covalent geometry : angle 0.52087 (16364) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.88566 ( 36) hydrogen bonds : bond 0.06002 ( 489) hydrogen bonds : angle 4.32264 ( 1422) link_ALPHA1-3 : bond 0.00808 ( 3) link_ALPHA1-3 : angle 1.91476 ( 9) link_ALPHA1-6 : bond 0.00697 ( 3) link_ALPHA1-6 : angle 1.90061 ( 9) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 1.91965 ( 27) link_BETA2-3 : bond 0.00132 ( 3) link_BETA2-3 : angle 3.16289 ( 9) link_NAG-ASN : bond 0.00678 ( 9) link_NAG-ASN : angle 3.91837 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9217 (mp0) REVERT: B 346 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: B 358 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 382 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7391 (ttpp) REVERT: B 464 MET cc_start: 0.8898 (mtm) cc_final: 0.8350 (mpt) REVERT: C 358 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 462 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6570 (mt-10) REVERT: C 464 MET cc_start: 0.8701 (mtm) cc_final: 0.8118 (mpt) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.7946 time to fit residues: 75.6631 Evaluate side-chains 90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 378 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 = 0.3067 r_free = 0.3067 target = 0.072712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.046407 restraints weight = 22674.527| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 2.68 r_work: 0.2353 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12113 Z= 0.133 Angle : 0.554 16.692 16481 Z= 0.274 Chirality : 0.045 0.681 1874 Planarity : 0.003 0.034 2104 Dihedral : 9.274 75.786 2216 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.95 % Allowed : 15.18 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1436 helix: 4.28 (0.24), residues: 333 sheet: 0.96 (0.29), residues: 325 loop : -0.85 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.020 0.001 TYR C 472 PHE 0.019 0.001 PHE C 502 TRP 0.007 0.001 TRP A 423 HIS 0.004 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00307 (12068) covalent geometry : angle 0.51609 (16364) SS BOND : bond 0.00199 ( 18) SS BOND : angle 0.87744 ( 36) hydrogen bonds : bond 0.05989 ( 489) hydrogen bonds : angle 4.32739 ( 1422) link_ALPHA1-3 : bond 0.00793 ( 3) link_ALPHA1-3 : angle 1.92486 ( 9) link_ALPHA1-6 : bond 0.00711 ( 3) link_ALPHA1-6 : angle 1.89696 ( 9) link_BETA1-4 : bond 0.00338 ( 9) link_BETA1-4 : angle 1.90787 ( 27) link_BETA2-3 : bond 0.00035 ( 3) link_BETA2-3 : angle 3.14575 ( 9) link_NAG-ASN : bond 0.00682 ( 9) link_NAG-ASN : angle 3.90947 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.91 seconds wall clock time: 88 minutes 17.71 seconds (5297.71 seconds total)