Starting phenix.real_space_refine on Wed Feb 4 08:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ky2_62636/02_2026/9ky2_62636.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 14 5.16 5 C 5913 2.51 5 N 1605 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9346 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2825 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "C" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "V" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 135 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TPO:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 135 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TPO:plan-1': 5} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.74, per 1000 atoms: 0.19 Number of scatterers: 9346 At special positions: 0 Unit cell: (83.9047, 136.472, 102.101, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 14 15.00 O 1800 8.00 N 1605 7.00 C 5913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " 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 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 225.9 milliseconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 6.2% alpha, 53.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.716A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.712A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 393 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.910A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE A 62 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 80 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR A 64 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS A 78 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LYS F 78 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR F 64 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 80 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE F 62 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE F 82 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL F 60 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU F 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN F 86 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL F 56 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N VAL F 143 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS F 171 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 291 removed outlier: 6.858A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE A 62 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 80 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TYR A 64 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS A 78 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LYS F 78 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR F 64 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 80 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE F 62 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE F 82 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL F 60 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU F 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN F 86 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL F 56 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU F 141 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.843A pdb=" N THR A 187 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.843A pdb=" N THR A 187 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.718A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 259 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 10 removed outlier: 5.601A pdb=" N GLY B 19 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.668A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 55 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N SER B 35 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 112 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.668A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 55 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N SER B 35 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.689A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.334A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.334A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 6 through 10 removed outlier: 5.490A pdb=" N GLY D 19 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 14 through 15 removed outlier: 8.898A pdb=" N SER D 35 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER D 55 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.594A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.532A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.372A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.372A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AC2, first strand: chain 'F' and resid 185 through 190 removed outlier: 3.611A pdb=" N ASN F 223 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 185 through 190 Processing sheet with id=AC4, first strand: chain 'F' and resid 208 through 210 removed outlier: 3.765A pdb=" N TYR F 322 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU F 344 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N VAL F 320 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS F 231 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN F 238 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA F 240 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS F 251 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE F 242 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN F 249 " --> pdb=" O ILE F 242 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3004 1.34 - 1.46: 2037 1.46 - 1.57: 4455 1.57 - 1.69: 44 1.69 - 1.81: 20 Bond restraints: 9560 Sorted by residual: bond pdb=" OG1 TPO U 335 " pdb=" P TPO U 335 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" OG1 TPO V 340 " pdb=" P TPO V 340 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO U 337 " pdb=" P TPO U 337 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO V 337 " pdb=" P TPO V 337 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO V 335 " pdb=" P TPO V 335 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12864 2.46 - 4.91: 110 4.91 - 7.37: 22 7.37 - 9.83: 10 9.83 - 12.28: 10 Bond angle restraints: 13016 Sorted by residual: angle pdb=" CB TPO U 337 " pdb=" OG1 TPO U 337 " pdb=" P TPO U 337 " ideal model delta sigma weight residual 119.31 107.03 12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" CB TPO V 337 " pdb=" OG1 TPO V 337 " pdb=" P TPO V 337 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO U 343 " pdb=" OG1 TPO U 343 " pdb=" P TPO U 343 " ideal model delta sigma weight residual 119.31 107.33 11.98 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB TPO U 340 " pdb=" OG1 TPO U 340 " pdb=" P TPO U 340 " ideal model delta sigma weight residual 119.31 107.49 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB TPO V 335 " pdb=" OG1 TPO V 335 " pdb=" P TPO V 335 " ideal model delta sigma weight residual 119.31 107.50 11.81 3.00e+00 1.11e-01 1.55e+01 ... (remaining 13011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 5175 16.16 - 32.32: 425 32.32 - 48.47: 93 48.47 - 64.63: 14 64.63 - 80.79: 11 Dihedral angle restraints: 5718 sinusoidal: 2219 harmonic: 3499 Sorted by residual: dihedral pdb=" CA ASN A 312 " pdb=" C ASN A 312 " pdb=" N LYS A 313 " pdb=" CA LYS A 313 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " pdb=" CZ ARG B 90 " ideal model delta sinusoidal sigma weight residual -180.00 -136.71 -43.29 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG D 90 " pdb=" CD ARG D 90 " pdb=" NE ARG D 90 " pdb=" CZ ARG D 90 " ideal model delta sinusoidal sigma weight residual -180.00 -137.51 -42.49 2 1.50e+01 4.44e-03 9.73e+00 ... (remaining 5715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 919 0.030 - 0.060: 348 0.060 - 0.090: 96 0.090 - 0.120: 95 0.120 - 0.150: 10 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CB TPO U 335 " pdb=" CA TPO U 335 " pdb=" OG1 TPO U 335 " pdb=" CG2 TPO U 335 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1465 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 14 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 15 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 14 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO F 15 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 15 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 15 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 124 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO F 125 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 125 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 125 " 0.019 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 700 2.74 - 3.28: 8753 3.28 - 3.82: 15701 3.82 - 4.36: 19178 4.36 - 4.90: 33532 Nonbonded interactions: 77864 Sorted by model distance: nonbonded pdb=" OD2 ASP F 261 " pdb=" OH TYR F 273 " model vdw 2.203 3.040 nonbonded pdb=" OD2 ASP A 261 " pdb=" OH TYR A 273 " model vdw 2.247 3.040 nonbonded pdb=" OG SER F 14 " pdb=" OD1 ASN F 16 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" OD2 ASP A 396 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 20 " pdb=" OD1 ASN B 87 " model vdw 2.290 3.040 ... (remaining 77859 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 7 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 311 or (resid 312 through 314 an \ d (name N or name CA or name C or name O or name CB )) or resid 315 through 408) \ ) selection = (chain 'F' and (resid 7 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 177 or (resid 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 408)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 5 through 121) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 65 or (resid 66 and (name N or name CA \ or name C or name O or name CB )) or resid 67 through 107)) } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.006 0.112 9564 Z= 0.288 Angle : 0.707 12.284 13024 Z= 0.309 Chirality : 0.042 0.150 1468 Planarity : 0.004 0.042 1656 Dihedral : 12.927 80.792 3454 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1157 helix: 1.27 (0.67), residues: 60 sheet: 0.13 (0.23), residues: 562 loop : 0.16 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 101 TYR 0.006 0.001 TYR C 92 PHE 0.015 0.001 PHE F 399 TRP 0.005 0.001 TRP B 106 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 9560) covalent geometry : angle 0.70696 (13016) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.53059 ( 8) hydrogen bonds : bond 0.22398 ( 357) hydrogen bonds : angle 9.46228 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7206 (tt0) cc_final: 0.6829 (tt0) REVERT: A 223 ASN cc_start: 0.7130 (t0) cc_final: 0.6928 (p0) REVERT: E 4 GLN cc_start: 0.8310 (mp10) cc_final: 0.7801 (mp10) REVERT: F 153 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8516 (mttp) REVERT: F 154 SER cc_start: 0.8041 (p) cc_final: 0.7438 (t) REVERT: U 342 ASP cc_start: 0.7464 (p0) cc_final: 0.7202 (p0) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.5017 time to fit residues: 161.7521 Evaluate side-chains 220 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 173 GLN A 220 HIS A 256 GLN A 259 GLN B 80 ASN B 115 GLN C 28 GLN C 39 GLN D 87 ASN D 115 GLN F 112 HIS F 131 GLN F 182 GLN F 199 HIS F 220 HIS F 223 ASN F 259 GLN F 262 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077865 restraints weight = 17926.202| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.55 r_work: 0.3025 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9564 Z= 0.292 Angle : 0.685 11.355 13024 Z= 0.346 Chirality : 0.046 0.185 1468 Planarity : 0.005 0.045 1656 Dihedral : 6.158 54.907 1333 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.72 % Favored : 96.11 % Rotamer: Outliers : 2.79 % Allowed : 15.67 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1157 helix: 1.12 (0.64), residues: 60 sheet: 0.18 (0.23), residues: 554 loop : 0.12 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 25 TYR 0.011 0.002 TYR C 92 PHE 0.016 0.002 PHE A 399 TRP 0.008 0.002 TRP D 113 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 9560) covalent geometry : angle 0.68198 (13016) SS BOND : bond 0.00828 ( 4) SS BOND : angle 2.48714 ( 8) hydrogen bonds : bond 0.04837 ( 357) hydrogen bonds : angle 6.50580 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8366 (tt0) cc_final: 0.8041 (tt0) REVERT: A 297 GLU cc_start: 0.8351 (pm20) cc_final: 0.8099 (pm20) REVERT: B 68 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8624 (tppp) REVERT: B 76 ASP cc_start: 0.8704 (t0) cc_final: 0.8423 (t0) REVERT: C 67 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8794 (ttp80) REVERT: D 32 VAL cc_start: 0.8744 (p) cc_final: 0.8505 (t) REVERT: E 18 ASP cc_start: 0.8010 (t70) cc_final: 0.7721 (t0) REVERT: E 91 GLN cc_start: 0.8953 (pp30) cc_final: 0.8680 (pp30) REVERT: E 106 GLU cc_start: 0.7327 (tp30) cc_final: 0.6825 (tp30) REVERT: E 107 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.7823 (pp) REVERT: F 66 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7436 (mtm110) REVERT: F 223 ASN cc_start: 0.7881 (t0) cc_final: 0.6937 (t0) REVERT: F 251 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8209 (pmtt) REVERT: U 342 ASP cc_start: 0.8703 (p0) cc_final: 0.8493 (p0) outliers start: 28 outliers final: 18 residues processed: 261 average time/residue: 0.4754 time to fit residues: 133.0839 Evaluate side-chains 239 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 201 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 223 ASN A 256 GLN B 80 ASN B 115 GLN D 80 ASN D 115 GLN F 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078439 restraints weight = 17758.171| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.56 r_work: 0.3037 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9564 Z= 0.188 Angle : 0.616 12.052 13024 Z= 0.308 Chirality : 0.044 0.214 1468 Planarity : 0.004 0.043 1656 Dihedral : 5.941 57.855 1333 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.28 % Favored : 96.54 % Rotamer: Outliers : 5.99 % Allowed : 16.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1157 helix: 1.24 (0.64), residues: 60 sheet: 0.21 (0.22), residues: 545 loop : 0.13 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 25 TYR 0.011 0.001 TYR A 250 PHE 0.011 0.002 PHE A 62 TRP 0.006 0.001 TRP B 50 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9560) covalent geometry : angle 0.61517 (13016) SS BOND : bond 0.00514 ( 4) SS BOND : angle 1.55020 ( 8) hydrogen bonds : bond 0.03985 ( 357) hydrogen bonds : angle 6.05857 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8884 (pp) REVERT: A 201 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 207 GLU cc_start: 0.8304 (tt0) cc_final: 0.7984 (tt0) REVERT: A 223 ASN cc_start: 0.7618 (t0) cc_final: 0.6701 (t0) REVERT: A 231 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8167 (mtmt) REVERT: A 239 TYR cc_start: 0.8396 (m-80) cc_final: 0.8061 (m-80) REVERT: A 251 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8202 (mttt) REVERT: A 284 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: B 68 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8649 (tppp) REVERT: B 76 ASP cc_start: 0.8702 (t0) cc_final: 0.8393 (t0) REVERT: D 32 VAL cc_start: 0.8809 (p) cc_final: 0.8590 (t) REVERT: E 18 ASP cc_start: 0.7951 (t70) cc_final: 0.7659 (t0) REVERT: E 106 GLU cc_start: 0.7131 (tp30) cc_final: 0.6601 (tp30) REVERT: E 107 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7730 (pp) REVERT: F 66 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7172 (mtm-85) REVERT: F 71 VAL cc_start: 0.8668 (m) cc_final: 0.8378 (t) REVERT: F 223 ASN cc_start: 0.7850 (t0) cc_final: 0.6902 (t0) REVERT: F 232 ILE cc_start: 0.8695 (mt) cc_final: 0.8437 (mp) REVERT: F 250 TYR cc_start: 0.8344 (m-80) cc_final: 0.7952 (m-80) REVERT: F 251 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8009 (pmtt) outliers start: 60 outliers final: 31 residues processed: 274 average time/residue: 0.4566 time to fit residues: 134.5309 Evaluate side-chains 262 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 98 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.0060 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 199 HIS A 220 HIS B 80 ASN B 115 GLN D 80 ASN D 115 GLN F 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079359 restraints weight = 17888.206| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.58 r_work: 0.3053 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9564 Z= 0.136 Angle : 0.594 13.911 13024 Z= 0.291 Chirality : 0.044 0.142 1468 Planarity : 0.004 0.039 1656 Dihedral : 5.772 59.867 1333 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.28 % Rotamer: Outliers : 4.39 % Allowed : 20.26 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1157 helix: 1.55 (0.66), residues: 60 sheet: 0.29 (0.22), residues: 542 loop : 0.28 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.019 0.001 TYR A 250 PHE 0.017 0.001 PHE D 30 TRP 0.005 0.001 TRP B 50 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9560) covalent geometry : angle 0.59330 (13016) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.31340 ( 8) hydrogen bonds : bond 0.03456 ( 357) hydrogen bonds : angle 5.68477 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8823 (pp) REVERT: A 148 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (ttp-170) REVERT: A 158 LYS cc_start: 0.8348 (pttp) cc_final: 0.7984 (pptt) REVERT: A 201 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 207 GLU cc_start: 0.8392 (tt0) cc_final: 0.8060 (tt0) REVERT: A 232 ILE cc_start: 0.8960 (mt) cc_final: 0.8593 (tt) REVERT: A 239 TYR cc_start: 0.8390 (m-80) cc_final: 0.8068 (m-80) REVERT: A 251 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8156 (mttt) REVERT: A 279 LEU cc_start: 0.9040 (tp) cc_final: 0.8761 (tt) REVERT: A 284 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: B 76 ASP cc_start: 0.8709 (t0) cc_final: 0.8381 (t0) REVERT: D 32 VAL cc_start: 0.8794 (p) cc_final: 0.8586 (t) REVERT: D 76 ASP cc_start: 0.8535 (t0) cc_final: 0.7996 (t0) REVERT: E 4 GLN cc_start: 0.8667 (mp10) cc_final: 0.8256 (mp10) REVERT: E 18 ASP cc_start: 0.7906 (t70) cc_final: 0.7612 (t0) REVERT: F 66 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7182 (mtm-85) REVERT: F 71 VAL cc_start: 0.8693 (m) cc_final: 0.8388 (t) REVERT: F 148 ARG cc_start: 0.9003 (ttm170) cc_final: 0.8737 (ttm170) REVERT: F 178 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8752 (mmmm) REVERT: F 223 ASN cc_start: 0.7905 (t0) cc_final: 0.6950 (t0) REVERT: F 231 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8296 (mtmt) REVERT: F 250 TYR cc_start: 0.8345 (m-80) cc_final: 0.8007 (m-80) REVERT: F 251 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7935 (pmtt) outliers start: 44 outliers final: 22 residues processed: 268 average time/residue: 0.4435 time to fit residues: 127.5332 Evaluate side-chains 248 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 84 optimal weight: 0.0670 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 220 HIS A 223 ASN B 80 ASN B 115 GLN C 28 GLN D 80 ASN D 115 GLN F 220 HIS F 256 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078477 restraints weight = 17965.597| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.56 r_work: 0.3037 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9564 Z= 0.169 Angle : 0.602 14.597 13024 Z= 0.297 Chirality : 0.044 0.139 1468 Planarity : 0.004 0.040 1656 Dihedral : 5.737 57.522 1333 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 5.19 % Allowed : 20.36 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1157 helix: 2.00 (0.71), residues: 54 sheet: 0.29 (0.22), residues: 545 loop : 0.30 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 25 TYR 0.018 0.001 TYR A 250 PHE 0.013 0.001 PHE F 116 TRP 0.005 0.001 TRP D 50 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9560) covalent geometry : angle 0.60176 (13016) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.30938 ( 8) hydrogen bonds : bond 0.03470 ( 357) hydrogen bonds : angle 5.49923 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8865 (pp) REVERT: A 158 LYS cc_start: 0.8237 (pttp) cc_final: 0.7839 (pptt) REVERT: A 207 GLU cc_start: 0.8384 (tt0) cc_final: 0.8097 (tt0) REVERT: A 223 ASN cc_start: 0.7682 (t0) cc_final: 0.6728 (t0) REVERT: A 231 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7972 (mttp) REVERT: A 232 ILE cc_start: 0.8941 (mt) cc_final: 0.8573 (tt) REVERT: A 284 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: B 76 ASP cc_start: 0.8706 (t0) cc_final: 0.8382 (t0) REVERT: D 76 ASP cc_start: 0.8513 (t0) cc_final: 0.8012 (t0) REVERT: E 4 GLN cc_start: 0.8667 (mp10) cc_final: 0.8287 (mp10) REVERT: E 18 ASP cc_start: 0.7931 (t70) cc_final: 0.7656 (t0) REVERT: E 43 LYS cc_start: 0.9103 (tppp) cc_final: 0.8772 (mmmm) REVERT: F 66 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: F 71 VAL cc_start: 0.8702 (m) cc_final: 0.8444 (t) REVERT: F 158 LYS cc_start: 0.8153 (pttp) cc_final: 0.7878 (pptt) REVERT: F 223 ASN cc_start: 0.7987 (t0) cc_final: 0.7098 (t0) REVERT: F 250 TYR cc_start: 0.8318 (m-80) cc_final: 0.8005 (m-80) REVERT: F 251 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7973 (pmtt) outliers start: 52 outliers final: 35 residues processed: 267 average time/residue: 0.4366 time to fit residues: 125.1696 Evaluate side-chains 265 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.0070 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 80 ASN B 115 GLN D 80 ASN D 115 GLN F 220 HIS F 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077886 restraints weight = 17985.770| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.50 r_work: 0.3035 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9564 Z= 0.197 Angle : 0.625 14.330 13024 Z= 0.309 Chirality : 0.044 0.141 1468 Planarity : 0.004 0.038 1656 Dihedral : 5.724 53.737 1333 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 4.69 % Allowed : 22.06 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1157 helix: 1.93 (0.71), residues: 54 sheet: 0.29 (0.22), residues: 544 loop : 0.29 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 25 TYR 0.022 0.001 TYR A 250 PHE 0.019 0.002 PHE B 30 TRP 0.006 0.001 TRP B 50 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9560) covalent geometry : angle 0.62445 (13016) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.37982 ( 8) hydrogen bonds : bond 0.03505 ( 357) hydrogen bonds : angle 5.50460 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 157 GLU cc_start: 0.8401 (tp30) cc_final: 0.8164 (tp30) REVERT: A 158 LYS cc_start: 0.8312 (pttp) cc_final: 0.7948 (pptt) REVERT: A 207 GLU cc_start: 0.8367 (tt0) cc_final: 0.8084 (tt0) REVERT: A 232 ILE cc_start: 0.8955 (mt) cc_final: 0.8573 (tt) REVERT: A 284 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: A 394 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6807 (t70) REVERT: B 76 ASP cc_start: 0.8716 (t0) cc_final: 0.8409 (t0) REVERT: D 14 LEU cc_start: 0.9072 (tp) cc_final: 0.8871 (tm) REVERT: D 76 ASP cc_start: 0.8492 (t0) cc_final: 0.7967 (t0) REVERT: E 4 GLN cc_start: 0.8744 (mp10) cc_final: 0.8390 (mp10) REVERT: E 18 ASP cc_start: 0.7903 (t70) cc_final: 0.7656 (t0) REVERT: E 106 GLU cc_start: 0.6918 (tp30) cc_final: 0.6446 (tp30) REVERT: F 66 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7183 (mtm-85) REVERT: F 71 VAL cc_start: 0.8685 (m) cc_final: 0.8458 (t) REVERT: F 158 LYS cc_start: 0.8132 (pttp) cc_final: 0.7908 (pptt) REVERT: F 166 ARG cc_start: 0.8553 (mtp180) cc_final: 0.8030 (mtp180) REVERT: F 250 TYR cc_start: 0.8269 (m-80) cc_final: 0.7923 (m-80) REVERT: F 251 LYS cc_start: 0.8314 (mtpp) cc_final: 0.7987 (pmtt) outliers start: 47 outliers final: 34 residues processed: 262 average time/residue: 0.4038 time to fit residues: 114.0149 Evaluate side-chains 259 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 223 ASN B 80 ASN B 115 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 220 HIS F 223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078140 restraints weight = 17933.693| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.56 r_work: 0.3037 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9564 Z= 0.173 Angle : 0.625 14.511 13024 Z= 0.307 Chirality : 0.044 0.141 1468 Planarity : 0.004 0.042 1656 Dihedral : 5.656 50.547 1333 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 4.39 % Allowed : 23.15 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1157 helix: 1.99 (0.72), residues: 54 sheet: 0.31 (0.22), residues: 544 loop : 0.27 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 25 TYR 0.023 0.001 TYR A 250 PHE 0.012 0.001 PHE F 116 TRP 0.006 0.001 TRP B 50 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9560) covalent geometry : angle 0.62465 (13016) SS BOND : bond 0.00205 ( 4) SS BOND : angle 1.28363 ( 8) hydrogen bonds : bond 0.03406 ( 357) hydrogen bonds : angle 5.44093 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 66 ARG cc_start: 0.8328 (pmm-80) cc_final: 0.8127 (pmm-80) REVERT: A 158 LYS cc_start: 0.8300 (pttp) cc_final: 0.7857 (pptt) REVERT: A 207 GLU cc_start: 0.8391 (tt0) cc_final: 0.8091 (tt0) REVERT: A 231 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7947 (mmmm) REVERT: A 232 ILE cc_start: 0.8923 (mt) cc_final: 0.8546 (tt) REVERT: A 284 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: B 76 ASP cc_start: 0.8734 (t0) cc_final: 0.8400 (t0) REVERT: D 14 LEU cc_start: 0.9053 (tp) cc_final: 0.8847 (tm) REVERT: D 76 ASP cc_start: 0.8468 (t0) cc_final: 0.7942 (t0) REVERT: E 4 GLN cc_start: 0.8741 (mp10) cc_final: 0.8400 (mp10) REVERT: E 18 ASP cc_start: 0.7895 (t70) cc_final: 0.7637 (t0) REVERT: E 106 GLU cc_start: 0.7166 (tp30) cc_final: 0.6642 (tp30) REVERT: F 66 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7212 (mtm-85) REVERT: F 71 VAL cc_start: 0.8684 (m) cc_final: 0.8458 (t) REVERT: F 72 LEU cc_start: 0.8897 (mt) cc_final: 0.8548 (mm) REVERT: F 158 LYS cc_start: 0.8281 (pttp) cc_final: 0.8052 (pptt) REVERT: F 166 ARG cc_start: 0.8551 (mtp180) cc_final: 0.7994 (mtp180) REVERT: F 250 TYR cc_start: 0.8317 (m-80) cc_final: 0.8019 (m-80) REVERT: F 251 LYS cc_start: 0.8321 (mtpp) cc_final: 0.8010 (pmtt) REVERT: F 295 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8729 (mmmm) outliers start: 44 outliers final: 34 residues processed: 255 average time/residue: 0.4201 time to fit residues: 115.3088 Evaluate side-chains 265 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 44 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 220 HIS A 223 ASN B 80 ASN B 115 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 220 HIS F 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077530 restraints weight = 17998.297| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.55 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9564 Z= 0.205 Angle : 0.647 14.421 13024 Z= 0.319 Chirality : 0.044 0.143 1468 Planarity : 0.005 0.050 1656 Dihedral : 5.680 48.531 1333 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 4.49 % Allowed : 23.65 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1157 helix: 1.98 (0.72), residues: 54 sheet: 0.33 (0.22), residues: 554 loop : 0.21 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 25 TYR 0.030 0.001 TYR A 239 PHE 0.019 0.002 PHE D 30 TRP 0.007 0.001 TRP B 50 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9560) covalent geometry : angle 0.64625 (13016) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.36990 ( 8) hydrogen bonds : bond 0.03491 ( 357) hydrogen bonds : angle 5.42928 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8909 (pp) REVERT: A 66 ARG cc_start: 0.8366 (pmm-80) cc_final: 0.8145 (pmm-80) REVERT: A 158 LYS cc_start: 0.8210 (pttp) cc_final: 0.7885 (pptt) REVERT: A 207 GLU cc_start: 0.8394 (tt0) cc_final: 0.8111 (tt0) REVERT: A 231 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7952 (mmmm) REVERT: A 232 ILE cc_start: 0.8913 (mt) cc_final: 0.8541 (tt) REVERT: A 284 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: A 394 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6812 (t70) REVERT: B 68 LYS cc_start: 0.8908 (tppp) cc_final: 0.8425 (tppp) REVERT: B 76 ASP cc_start: 0.8757 (t0) cc_final: 0.8421 (t0) REVERT: D 14 LEU cc_start: 0.9060 (tp) cc_final: 0.8859 (tm) REVERT: D 76 ASP cc_start: 0.8479 (t0) cc_final: 0.7944 (t0) REVERT: E 4 GLN cc_start: 0.8778 (mp10) cc_final: 0.8429 (mp10) REVERT: E 18 ASP cc_start: 0.7947 (t70) cc_final: 0.7688 (t0) REVERT: E 106 GLU cc_start: 0.7176 (tp30) cc_final: 0.6698 (tp30) REVERT: F 66 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: F 71 VAL cc_start: 0.8721 (m) cc_final: 0.8486 (t) REVERT: F 146 GLU cc_start: 0.8206 (tt0) cc_final: 0.7501 (tt0) REVERT: F 158 LYS cc_start: 0.8337 (pttp) cc_final: 0.8084 (pptt) REVERT: F 166 ARG cc_start: 0.8548 (mtp180) cc_final: 0.8087 (mtp180) REVERT: F 177 GLU cc_start: 0.8589 (mp0) cc_final: 0.8368 (mp0) REVERT: F 250 TYR cc_start: 0.8276 (m-80) cc_final: 0.7969 (m-80) REVERT: F 251 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8010 (pmtt) REVERT: F 295 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8553 (mmmm) outliers start: 45 outliers final: 35 residues processed: 251 average time/residue: 0.4369 time to fit residues: 118.3491 Evaluate side-chains 258 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 112 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 30 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 223 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 115 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 220 HIS F 223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.079630 restraints weight = 17658.016| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.54 r_work: 0.3066 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9564 Z= 0.126 Angle : 0.626 14.937 13024 Z= 0.306 Chirality : 0.044 0.135 1468 Planarity : 0.005 0.054 1656 Dihedral : 5.500 48.008 1333 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 3.89 % Allowed : 24.35 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1157 helix: 2.07 (0.72), residues: 54 sheet: 0.44 (0.22), residues: 539 loop : 0.23 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 25 TYR 0.026 0.001 TYR F 64 PHE 0.021 0.001 PHE D 30 TRP 0.005 0.001 TRP B 50 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9560) covalent geometry : angle 0.62562 (13016) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.90398 ( 8) hydrogen bonds : bond 0.03187 ( 357) hydrogen bonds : angle 5.24069 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8728 (pp) REVERT: A 66 ARG cc_start: 0.8275 (pmm-80) cc_final: 0.8062 (pmm-80) REVERT: A 207 GLU cc_start: 0.8392 (tt0) cc_final: 0.8068 (tt0) REVERT: A 231 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7900 (mmmm) REVERT: A 232 ILE cc_start: 0.8877 (mt) cc_final: 0.8507 (tt) REVERT: A 284 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: A 394 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6768 (t70) REVERT: B 68 LYS cc_start: 0.8899 (tppp) cc_final: 0.8414 (tppp) REVERT: B 76 ASP cc_start: 0.8766 (t0) cc_final: 0.8414 (t0) REVERT: D 14 LEU cc_start: 0.9018 (tp) cc_final: 0.8806 (tm) REVERT: D 76 ASP cc_start: 0.8481 (t0) cc_final: 0.7934 (t0) REVERT: E 4 GLN cc_start: 0.8684 (mp10) cc_final: 0.8352 (mp10) REVERT: E 18 ASP cc_start: 0.7916 (t70) cc_final: 0.7651 (t0) REVERT: E 106 GLU cc_start: 0.7183 (tp30) cc_final: 0.6731 (tp30) REVERT: F 66 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: F 71 VAL cc_start: 0.8699 (m) cc_final: 0.8457 (t) REVERT: F 158 LYS cc_start: 0.8364 (pttp) cc_final: 0.8072 (pptt) REVERT: F 177 GLU cc_start: 0.8585 (mp0) cc_final: 0.8331 (mp0) REVERT: F 223 ASN cc_start: 0.7752 (t0) cc_final: 0.7023 (t0) REVERT: F 250 TYR cc_start: 0.8246 (m-80) cc_final: 0.7910 (m-80) REVERT: F 251 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7840 (pmtt) REVERT: F 295 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8690 (mmmm) outliers start: 39 outliers final: 24 residues processed: 257 average time/residue: 0.4295 time to fit residues: 119.0115 Evaluate side-chains 258 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 115 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN F 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079271 restraints weight = 17918.863| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.55 r_work: 0.3059 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9564 Z= 0.151 Angle : 0.646 14.347 13024 Z= 0.319 Chirality : 0.044 0.138 1468 Planarity : 0.005 0.066 1656 Dihedral : 5.459 47.174 1333 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 3.09 % Allowed : 26.15 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1157 helix: 2.11 (0.72), residues: 54 sheet: 0.46 (0.22), residues: 537 loop : 0.26 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 25 TYR 0.025 0.001 TYR F 64 PHE 0.020 0.001 PHE D 30 TRP 0.006 0.001 TRP B 50 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9560) covalent geometry : angle 0.64570 (13016) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.08556 ( 8) hydrogen bonds : bond 0.03220 ( 357) hydrogen bonds : angle 5.22301 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.226 Fit side-chains REVERT: A 49 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8751 (pp) REVERT: A 66 ARG cc_start: 0.8288 (pmm-80) cc_final: 0.8082 (pmm-80) REVERT: A 186 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8126 (tp30) REVERT: A 207 GLU cc_start: 0.8390 (tt0) cc_final: 0.8062 (tt0) REVERT: A 231 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7949 (mmmm) REVERT: A 232 ILE cc_start: 0.8835 (mt) cc_final: 0.8457 (tt) REVERT: B 68 LYS cc_start: 0.8920 (tppp) cc_final: 0.8457 (tppp) REVERT: B 76 ASP cc_start: 0.8782 (t0) cc_final: 0.8445 (t0) REVERT: D 14 LEU cc_start: 0.9019 (tp) cc_final: 0.8807 (tm) REVERT: D 76 ASP cc_start: 0.8502 (t0) cc_final: 0.7959 (t0) REVERT: E 4 GLN cc_start: 0.8717 (mp10) cc_final: 0.8397 (mp10) REVERT: E 18 ASP cc_start: 0.7915 (t70) cc_final: 0.7647 (t0) REVERT: E 106 GLU cc_start: 0.7196 (tp30) cc_final: 0.6722 (tp30) REVERT: F 66 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7276 (mtm-85) REVERT: F 71 VAL cc_start: 0.8797 (m) cc_final: 0.8558 (t) REVERT: F 146 GLU cc_start: 0.8210 (tt0) cc_final: 0.7347 (tt0) REVERT: F 148 ARG cc_start: 0.8912 (ttm170) cc_final: 0.8632 (ttm170) REVERT: F 158 LYS cc_start: 0.8358 (pttp) cc_final: 0.8044 (pptt) REVERT: F 166 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7955 (mtp180) REVERT: F 223 ASN cc_start: 0.7760 (t0) cc_final: 0.6954 (t0) REVERT: F 231 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8371 (mtmt) REVERT: F 250 TYR cc_start: 0.8265 (m-80) cc_final: 0.7920 (m-80) REVERT: F 251 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7889 (pmtt) REVERT: F 295 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8560 (mmmm) outliers start: 31 outliers final: 26 residues processed: 252 average time/residue: 0.4215 time to fit residues: 114.4795 Evaluate side-chains 264 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 223 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 115 GLN C 101 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 115 GLN F 220 HIS F 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078189 restraints weight = 17652.325| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.53 r_work: 0.3041 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9564 Z= 0.193 Angle : 0.674 14.273 13024 Z= 0.332 Chirality : 0.045 0.149 1468 Planarity : 0.005 0.063 1656 Dihedral : 5.532 46.588 1333 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 2.99 % Allowed : 26.05 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1157 helix: 2.11 (0.73), residues: 54 sheet: 0.40 (0.22), residues: 531 loop : 0.26 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 25 TYR 0.028 0.001 TYR F 64 PHE 0.022 0.002 PHE D 30 TRP 0.007 0.001 TRP B 50 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9560) covalent geometry : angle 0.67367 (13016) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.22237 ( 8) hydrogen bonds : bond 0.03379 ( 357) hydrogen bonds : angle 5.36825 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3332.11 seconds wall clock time: 57 minutes 25.68 seconds (3445.68 seconds total)