Starting phenix.real_space_refine on Tue Jun 10 16:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw5_60516/06_2025/8zw5_60516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw5_60516/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zw5_60516/06_2025/8zw5_60516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw5_60516/06_2025/8zw5_60516.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw5_60516/06_2025/8zw5_60516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw5_60516/06_2025/8zw5_60516.cif" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.20, per 1000 atoms: 0.69 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: 4.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 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: 2.73 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: 5.05 Time building geometry restraints manager: 4.58 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 502 \ or resid 601)) selection = (chain 'B' and (resid 12 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 327 or resid 337 through 502 or \ resid 601)) selection = (chain 'C' and (resid 12 through 462 or (resid 463 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 464 through 502 or resid 601)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.380 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), 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 TRP 0.009 0.001 TRP B 423 HIS 0.008 0.001 HIS B 473 PHE 0.014 0.001 PHE C 355 TYR 0.010 0.001 TYR C 107 ARG 0.003 0.000 ARG C 64 Details of bonding type rmsd 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) 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_ALPHA1-3 : bond 0.00210 ( 3) link_ALPHA1-3 : angle 1.97274 ( 9) hydrogen bonds : bond 0.13071 ( 489) hydrogen bonds : angle 5.96532 ( 1422) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.03490 ( 36) covalent geometry : bond 0.00343 (12068) covalent geometry : angle 0.63294 (16364) *********************** 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 : 1.454 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: 1.6806 time to fit residues: 251.3512 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 : 1.312 ------------------------------------------------------------------------------- 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 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.072306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.046005 restraints weight = 22188.849| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 2.62 r_work: 0.2326 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12113 Z= 0.210 Angle : 0.611 20.965 16481 Z= 0.304 Chirality : 0.049 0.859 1874 Planarity : 0.004 0.039 2104 Dihedral : 11.730 87.379 2227 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.29 % Allowed : 12.96 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1436 helix: 3.42 (0.25), residues: 335 sheet: 0.62 (0.28), residues: 327 loop : -1.12 (0.18), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.007 0.001 HIS B 473 PHE 0.013 0.002 PHE C 355 TYR 0.025 0.001 TYR C 472 ARG 0.005 0.000 ARG C 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00190 ( 3) link_BETA2-3 : angle 4.27469 ( 9) link_NAG-ASN : bond 0.00709 ( 9) link_NAG-ASN : angle 4.78370 ( 27) link_ALPHA1-6 : bond 0.00219 ( 3) link_ALPHA1-6 : angle 2.01246 ( 9) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 2.23110 ( 27) link_ALPHA1-3 : bond 0.00613 ( 3) link_ALPHA1-3 : angle 1.78587 ( 9) hydrogen bonds : bond 0.07203 ( 489) hydrogen bonds : angle 5.00821 ( 1422) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.03303 ( 36) covalent geometry : bond 0.00505 (12068) covalent geometry : angle 0.56051 (16364) *********************** 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 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.8428 (ptm160) cc_final: 0.8225 (mtm180) REVERT: A 342 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: A 464 MET cc_start: 0.9056 (mtm) cc_final: 0.8694 (mtm) REVERT: B 212 GLN cc_start: 0.9575 (OUTLIER) cc_final: 0.8995 (pt0) REVERT: B 454 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8041 (ttp-170) REVERT: B 464 MET cc_start: 0.9104 (mtm) cc_final: 0.8868 (mtm) REVERT: C 462 GLU cc_start: 0.7262 (tt0) cc_final: 0.7000 (mt-10) REVERT: C 472 TYR cc_start: 0.8667 (m-80) cc_final: 0.7990 (m-80) outliers start: 29 outliers final: 14 residues processed: 113 average time/residue: 1.6951 time to fit residues: 204.9262 Evaluate side-chains 101 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 342 GLU 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 90 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.072877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.046954 restraints weight = 22391.807| |-----------------------------------------------------------------------------| r_work (start): 0.2476 rms_B_bonded: 2.61 r_work: 0.2348 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12113 Z= 0.138 Angle : 0.551 18.228 16481 Z= 0.273 Chirality : 0.046 0.741 1874 Planarity : 0.003 0.043 2104 Dihedral : 11.069 82.528 2222 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.82 % Allowed : 12.96 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1436 helix: 3.75 (0.25), residues: 335 sheet: 0.73 (0.28), residues: 327 loop : -1.08 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 423 HIS 0.005 0.001 HIS B 473 PHE 0.011 0.001 PHE C 355 TYR 0.036 0.001 TYR B 472 ARG 0.010 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00069 ( 3) link_BETA2-3 : angle 3.82252 ( 9) link_NAG-ASN : bond 0.00740 ( 9) link_NAG-ASN : angle 4.23391 ( 27) link_ALPHA1-6 : bond 0.00502 ( 3) link_ALPHA1-6 : angle 1.92716 ( 9) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 2.07520 ( 27) link_ALPHA1-3 : bond 0.00734 ( 3) link_ALPHA1-3 : angle 1.71722 ( 9) hydrogen bonds : bond 0.06556 ( 489) hydrogen bonds : angle 4.70657 ( 1422) SS BOND : bond 0.00315 ( 18) SS BOND : angle 0.92869 ( 36) covalent geometry : bond 0.00314 (12068) covalent geometry : angle 0.50515 (16364) *********************** 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: 23 poor density : 86 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 464 MET cc_start: 0.9123 (mtm) cc_final: 0.8780 (mtm) REVERT: B 212 GLN cc_start: 0.9546 (OUTLIER) cc_final: 0.8890 (pt0) REVERT: B 454 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8102 (ttp-170) REVERT: C 277 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 462 GLU cc_start: 0.7242 (tt0) cc_final: 0.6926 (mt-10) REVERT: C 472 TYR cc_start: 0.8625 (m-80) cc_final: 0.8159 (m-10) outliers start: 23 outliers final: 12 residues processed: 104 average time/residue: 1.6721 time to fit residues: 186.8187 Evaluate side-chains 95 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 444 SER Chi-restraints excluded: chain B residue 454 ARG 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 125 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 0.0170 chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.071958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.045575 restraints weight = 22281.211| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 2.65 r_work: 0.2327 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12113 Z= 0.203 Angle : 0.585 19.147 16481 Z= 0.290 Chirality : 0.048 0.780 1874 Planarity : 0.003 0.042 2104 Dihedral : 10.857 81.814 2220 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.74 % Allowed : 13.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1436 helix: 3.89 (0.24), residues: 333 sheet: 0.75 (0.28), residues: 327 loop : -1.11 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 352 HIS 0.005 0.001 HIS B 473 PHE 0.012 0.001 PHE B 502 TYR 0.028 0.001 TYR B 472 ARG 0.006 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00123 ( 3) link_BETA2-3 : angle 3.78813 ( 9) link_NAG-ASN : bond 0.00710 ( 9) link_NAG-ASN : angle 4.43213 ( 27) link_ALPHA1-6 : bond 0.00430 ( 3) link_ALPHA1-6 : angle 1.97382 ( 9) link_BETA1-4 : bond 0.00281 ( 9) link_BETA1-4 : angle 2.12760 ( 27) link_ALPHA1-3 : bond 0.00641 ( 3) link_ALPHA1-3 : angle 1.79180 ( 9) hydrogen bonds : bond 0.06843 ( 489) hydrogen bonds : angle 4.66828 ( 1422) SS BOND : bond 0.00265 ( 18) SS BOND : angle 0.93354 ( 36) covalent geometry : bond 0.00488 (12068) covalent geometry : angle 0.53923 (16364) *********************** 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 107 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 464 MET cc_start: 0.9186 (mtm) cc_final: 0.8898 (mtm) REVERT: B 212 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8874 (pt0) REVERT: B 382 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7461 (ttpp) REVERT: B 454 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8145 (ttp-170) REVERT: B 464 MET cc_start: 0.9135 (mtm) cc_final: 0.8915 (mtm) REVERT: C 212 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: C 277 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8581 (mm-30) REVERT: C 462 GLU cc_start: 0.7353 (tt0) cc_final: 0.7120 (mt-10) REVERT: C 472 TYR cc_start: 0.8699 (m-80) cc_final: 0.8377 (m-10) outliers start: 22 outliers final: 11 residues processed: 104 average time/residue: 1.6900 time to fit residues: 189.2662 Evaluate side-chains 100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.072249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.045988 restraints weight = 22434.536| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 2.64 r_work: 0.2336 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2220 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1537 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= 0.140 Angle : 0.547 18.085 16481 Z= 0.271 Chirality : 0.046 0.732 1874 Planarity : 0.003 0.033 2104 Dihedral : 10.495 78.402 2220 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.34 % Allowed : 13.36 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1436 helix: 4.02 (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 TRP 0.009 0.001 TRP A 352 HIS 0.005 0.001 HIS B 473 PHE 0.012 0.001 PHE B 502 TYR 0.023 0.001 TYR B 472 ARG 0.005 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00055 ( 3) link_BETA2-3 : angle 3.51680 ( 9) link_NAG-ASN : bond 0.00715 ( 9) link_NAG-ASN : angle 4.20344 ( 27) link_ALPHA1-6 : bond 0.00554 ( 3) link_ALPHA1-6 : angle 1.90951 ( 9) link_BETA1-4 : bond 0.00360 ( 9) link_BETA1-4 : angle 2.02222 ( 27) link_ALPHA1-3 : bond 0.00733 ( 3) link_ALPHA1-3 : angle 1.79623 ( 9) hydrogen bonds : bond 0.06446 ( 489) hydrogen bonds : angle 4.53269 ( 1422) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.89458 ( 36) covalent geometry : bond 0.00320 (12068) covalent geometry : angle 0.50331 (16364) *********************** 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 : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 464 MET cc_start: 0.9173 (mtm) cc_final: 0.8874 (mtm) REVERT: B 212 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8855 (pt0) REVERT: B 382 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7439 (ttpp) REVERT: C 212 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.8710 (pt0) REVERT: C 277 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8587 (mm-30) REVERT: C 462 GLU cc_start: 0.7464 (tt0) cc_final: 0.7211 (mt-10) REVERT: C 472 TYR cc_start: 0.8689 (m-80) cc_final: 0.8431 (m-80) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 2.0563 time to fit residues: 212.7284 Evaluate side-chains 94 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 C residue 212 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 131 optimal weight: 0.0170 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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** ** 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 = 0.3051 r_free = 0.3051 target = 0.071915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.045614 restraints weight = 22612.161| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 2.64 r_work: 0.2330 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2216 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1631 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= 0.157 Angle : 0.558 18.038 16481 Z= 0.276 Chirality : 0.046 0.729 1874 Planarity : 0.003 0.034 2104 Dihedral : 10.258 77.473 2220 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.50 % Allowed : 13.75 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1436 helix: 4.10 (0.24), residues: 333 sheet: 0.85 (0.29), residues: 327 loop : -1.04 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 352 HIS 0.004 0.001 HIS C 357 PHE 0.015 0.001 PHE B 502 TYR 0.023 0.001 TYR B 472 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00133 ( 3) link_BETA2-3 : angle 3.48849 ( 9) link_NAG-ASN : bond 0.00715 ( 9) link_NAG-ASN : angle 4.19414 ( 27) link_ALPHA1-6 : bond 0.00563 ( 3) link_ALPHA1-6 : angle 1.90520 ( 9) link_BETA1-4 : bond 0.00326 ( 9) link_BETA1-4 : angle 2.02365 ( 27) link_ALPHA1-3 : bond 0.00715 ( 3) link_ALPHA1-3 : angle 1.83135 ( 9) hydrogen bonds : bond 0.06457 ( 489) hydrogen bonds : angle 4.49078 ( 1422) SS BOND : bond 0.00230 ( 18) SS BOND : angle 0.93361 ( 36) covalent geometry : bond 0.00371 (12068) covalent geometry : angle 0.51511 (16364) *********************** 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 100 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 212 GLN cc_start: 0.9567 (OUTLIER) cc_final: 0.8848 (pt0) REVERT: B 342 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9161 (mp0) REVERT: B 358 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 382 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7443 (ttpp) REVERT: C 212 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: C 277 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8481 (mm-30) REVERT: C 462 GLU cc_start: 0.7405 (tt0) cc_final: 0.7150 (mt-10) outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 1.4027 time to fit residues: 145.8610 Evaluate side-chains 92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 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 C residue 212 GLN Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.072604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.046217 restraints weight = 22633.621| |-----------------------------------------------------------------------------| r_work (start): 0.2470 rms_B_bonded: 2.67 r_work: 0.2341 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2226 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1686 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= 0.132 Angle : 0.550 17.316 16481 Z= 0.272 Chirality : 0.045 0.697 1874 Planarity : 0.003 0.033 2104 Dihedral : 9.906 76.894 2219 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.58 % Allowed : 14.07 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1436 helix: 4.20 (0.24), residues: 333 sheet: 0.87 (0.29), residues: 325 loop : -0.96 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 352 HIS 0.004 0.001 HIS C 357 PHE 0.013 0.001 PHE B 502 TYR 0.030 0.001 TYR C 472 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00050 ( 3) link_BETA2-3 : angle 3.32412 ( 9) link_NAG-ASN : bond 0.00708 ( 9) link_NAG-ASN : angle 4.03908 ( 27) link_ALPHA1-6 : bond 0.00649 ( 3) link_ALPHA1-6 : angle 1.88694 ( 9) link_BETA1-4 : bond 0.00364 ( 9) link_BETA1-4 : angle 1.96746 ( 27) link_ALPHA1-3 : bond 0.00781 ( 3) link_ALPHA1-3 : angle 1.83717 ( 9) hydrogen bonds : bond 0.06213 ( 489) hydrogen bonds : angle 4.41010 ( 1422) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.91852 ( 36) covalent geometry : bond 0.00302 (12068) covalent geometry : angle 0.50966 (16364) *********************** 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 104 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8976 (ttm) REVERT: A 358 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 464 MET cc_start: 0.9084 (mtm) cc_final: 0.8835 (mtm) REVERT: B 342 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9159 (mp0) REVERT: B 346 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: B 358 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 382 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7468 (ttpp) REVERT: B 464 MET cc_start: 0.8957 (mtm) cc_final: 0.8365 (mpt) REVERT: C 212 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: C 462 GLU cc_start: 0.7213 (tt0) cc_final: 0.6944 (mt-10) REVERT: C 464 MET cc_start: 0.8862 (mtm) cc_final: 0.8130 (mpt) REVERT: C 470 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8094 (tttm) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 1.4379 time to fit residues: 155.9246 Evaluate side-chains 97 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 348 MET 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 346 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.071550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.045169 restraints weight = 22649.973| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 2.66 r_work: 0.2318 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2204 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12113 Z= 0.202 Angle : 0.591 18.286 16481 Z= 0.293 Chirality : 0.047 0.739 1874 Planarity : 0.003 0.034 2104 Dihedral : 9.915 77.142 2216 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.19 % Allowed : 14.23 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1436 helix: 4.16 (0.24), residues: 333 sheet: 0.82 (0.29), residues: 327 loop : -1.05 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 352 HIS 0.005 0.001 HIS C 357 PHE 0.018 0.001 PHE B 502 TYR 0.031 0.001 TYR C 472 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_BETA2-3 : bond 0.00141 ( 3) link_BETA2-3 : angle 3.54694 ( 9) link_NAG-ASN : bond 0.00725 ( 9) link_NAG-ASN : angle 4.25552 ( 27) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 1.93111 ( 9) link_BETA1-4 : bond 0.00266 ( 9) link_BETA1-4 : angle 2.08570 ( 27) link_ALPHA1-3 : bond 0.00641 ( 3) link_ALPHA1-3 : angle 1.91164 ( 9) hydrogen bonds : bond 0.06651 ( 489) hydrogen bonds : angle 4.49107 ( 1422) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.93774 ( 36) covalent geometry : bond 0.00486 (12068) covalent geometry : angle 0.54895 (16364) *********************** 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 96 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 464 MET cc_start: 0.9118 (mtm) cc_final: 0.8882 (mtm) REVERT: B 342 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9185 (mp0) REVERT: B 346 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 358 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 382 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7508 (ttpp) REVERT: B 464 MET cc_start: 0.8971 (mtm) cc_final: 0.8370 (mpt) REVERT: C 212 GLN cc_start: 0.9569 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: C 462 GLU cc_start: 0.7243 (tt0) cc_final: 0.6983 (mt-10) REVERT: C 464 MET cc_start: 0.8893 (mtm) cc_final: 0.8157 (mpt) REVERT: C 470 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8178 (tttt) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 1.7352 time to fit residues: 173.2338 Evaluate side-chains 93 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain B residue 444 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3052 r_free = 0.3052 target = 0.071986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.045633 restraints weight = 22558.755| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 2.66 r_work: 0.2329 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2214 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12113 Z= 0.155 Angle : 0.568 17.700 16481 Z= 0.281 Chirality : 0.046 0.715 1874 Planarity : 0.003 0.034 2104 Dihedral : 9.781 76.991 2216 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.11 % Allowed : 14.39 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1436 helix: 4.19 (0.24), residues: 333 sheet: 0.85 (0.29), residues: 327 loop : -1.01 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 352 HIS 0.004 0.001 HIS C 357 PHE 0.015 0.001 PHE B 502 TYR 0.028 0.001 TYR C 472 ARG 0.004 0.000 ARG C 263 Details of bonding type rmsd link_BETA2-3 : bond 0.00030 ( 3) link_BETA2-3 : angle 3.42747 ( 9) link_NAG-ASN : bond 0.00717 ( 9) link_NAG-ASN : angle 4.13112 ( 27) link_ALPHA1-6 : bond 0.00607 ( 3) link_ALPHA1-6 : angle 1.85404 ( 9) link_BETA1-4 : bond 0.00328 ( 9) link_BETA1-4 : angle 2.02559 ( 27) link_ALPHA1-3 : bond 0.00707 ( 3) link_ALPHA1-3 : angle 1.87674 ( 9) hydrogen bonds : bond 0.06432 ( 489) hydrogen bonds : angle 4.44633 ( 1422) SS BOND : bond 0.00220 ( 18) SS BOND : angle 0.91219 ( 36) covalent geometry : bond 0.00363 (12068) covalent geometry : angle 0.52729 (16364) *********************** 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 95 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 212 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.8828 (pt0) REVERT: B 342 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9191 (mp0) REVERT: B 346 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: B 358 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 382 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7479 (ttpp) REVERT: C 212 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.8698 (pt0) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 1.4913 time to fit residues: 149.7388 Evaluate side-chains 92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain B residue 444 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.046696 restraints weight = 22359.340| |-----------------------------------------------------------------------------| r_work (start): 0.2487 rms_B_bonded: 2.67 r_work: 0.2360 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2244 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1851 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= 0.119 Angle : 0.550 16.493 16481 Z= 0.272 Chirality : 0.045 0.672 1874 Planarity : 0.003 0.033 2104 Dihedral : 9.378 76.160 2216 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.03 % Allowed : 14.62 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1436 helix: 4.33 (0.24), residues: 333 sheet: 0.94 (0.29), residues: 325 loop : -0.88 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 423 HIS 0.005 0.001 HIS C 473 PHE 0.018 0.001 PHE B 502 TYR 0.028 0.001 TYR C 472 ARG 0.004 0.000 ARG C 263 Details of bonding type rmsd link_BETA2-3 : bond 0.00029 ( 3) link_BETA2-3 : angle 3.14149 ( 9) link_NAG-ASN : bond 0.00685 ( 9) link_NAG-ASN : angle 3.86859 ( 27) link_ALPHA1-6 : bond 0.00723 ( 3) link_ALPHA1-6 : angle 1.87199 ( 9) link_BETA1-4 : bond 0.00372 ( 9) link_BETA1-4 : angle 1.90946 ( 27) link_ALPHA1-3 : bond 0.00826 ( 3) link_ALPHA1-3 : angle 1.84681 ( 9) hydrogen bonds : bond 0.05949 ( 489) hydrogen bonds : angle 4.30973 ( 1422) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.89549 ( 36) covalent geometry : bond 0.00267 (12068) covalent geometry : angle 0.51283 (16364) ********************** 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 96 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 342 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9217 (mp0) REVERT: B 346 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: B 358 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 382 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7425 (ttpp) REVERT: C 358 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 462 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6821 (mt-10) REVERT: C 464 MET cc_start: 0.8552 (mtm) cc_final: 0.8010 (mpt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 1.6141 time to fit residues: 163.4217 Evaluate side-chains 89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 50 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 133 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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 378 GLN ** 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 = 0.3064 r_free = 0.3064 target = 0.072460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.046674 restraints weight = 22424.306| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 2.59 r_work: 0.2353 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1852 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= 0.142 Angle : 0.559 16.819 16481 Z= 0.277 Chirality : 0.046 0.685 1874 Planarity : 0.003 0.033 2104 Dihedral : 9.331 76.143 2216 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.03 % Allowed : 14.86 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1436 helix: 4.30 (0.24), residues: 333 sheet: 0.92 (0.29), residues: 321 loop : -0.85 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.004 0.001 HIS C 357 PHE 0.014 0.001 PHE C 502 TYR 0.034 0.001 TYR C 472 ARG 0.004 0.000 ARG C 263 Details of bonding type rmsd link_BETA2-3 : bond 0.00068 ( 3) link_BETA2-3 : angle 3.19645 ( 9) link_NAG-ASN : bond 0.00684 ( 9) link_NAG-ASN : angle 3.93688 ( 27) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.90499 ( 9) link_BETA1-4 : bond 0.00326 ( 9) link_BETA1-4 : angle 1.93324 ( 27) link_ALPHA1-3 : bond 0.00787 ( 3) link_ALPHA1-3 : angle 1.92652 ( 9) hydrogen bonds : bond 0.06072 ( 489) hydrogen bonds : angle 4.33396 ( 1422) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.88438 ( 36) covalent geometry : bond 0.00331 (12068) covalent geometry : angle 0.52131 (16364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11431.25 seconds wall clock time: 199 minutes 46.12 seconds (11986.12 seconds total)