Starting phenix.real_space_refine on Tue Nov 18 04:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ce9_7462/11_2025/6ce9_7462.map" } resolution = 4.3 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= 0.003 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 6828 2.51 5 N 1806 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10782 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "B" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "M" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "L" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "N" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "P" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.83, per 1000 atoms: 0.26 Number of scatterers: 10782 At special positions: 0 Unit cell: (95.7, 150.7, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2056 8.00 N 1806 7.00 C 6828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.02 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG Q 1 " - " NAG Q 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG G 1 " - " FUC G 2 " " NAG H 1 " - " FUC H 3 " " NAG J 1 " - " FUC J 3 " " NAG R 1 " - " FUC R 2 " NAG-ASN " NAG A1014 " - " ASN A 16 " " NAG B1014 " - " ASN B 16 " " NAG C 1 " - " ASN A 25 " " NAG D 1 " - " ASN A 111 " " NAG E 1 " - " ASN A 255 " " NAG F 1 " - " ASN A 397 " " NAG G 1 " - " ASN A 418 " " NAG H 1 " - " ASN B 25 " " NAG I 1 " - " ASN B 111 " " NAG J 1 " - " ASN B 255 " " NAG Q 1 " - " ASN B 397 " " NAG R 1 " - " ASN B 418 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 507.6 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 19.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.252A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.542A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.514A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 143 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.939A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.544A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.252A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.541A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.513A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 143 " --> pdb=" O VAL B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.939A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.543A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'M' and resid 692 through 715 removed outlier: 3.905A pdb=" N LEU M 696 " --> pdb=" O ILE M 692 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER M 700 " --> pdb=" O LEU M 696 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 709 " --> pdb=" O PHE M 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS M 710 " --> pdb=" O GLU M 706 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL M 715 " --> pdb=" O ASN M 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 18 removed outlier: 3.739A pdb=" N ASN K 18 " --> pdb=" O TYR K 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 12 through 18 removed outlier: 3.737A pdb=" N ASN N 18 " --> pdb=" O TYR N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 Processing helix chain 'P' and resid 692 through 715 removed outlier: 3.905A pdb=" N LEU P 696 " --> pdb=" O ILE P 692 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER P 700 " --> pdb=" O LEU P 696 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 709 " --> pdb=" O PHE P 705 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS P 710 " --> pdb=" O GLU P 706 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL P 715 " --> pdb=" O ASN P 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.650A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 4.736A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.566A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 removed outlier: 3.661A pdb=" N ARG A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.584A pdb=" N ILE A 336 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.724A pdb=" N GLU A 471 " --> pdb=" O LYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AB4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.650A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 65 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS B 144 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB6, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'B' and resid 212 through 216 removed outlier: 4.735A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.566A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.661A pdb=" N ARG B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AC3, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.585A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.724A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AC6, first strand: chain 'B' and resid 532 through 534 226 hydrogen bonds defined for protein. 588 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: 1.62 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3437 1.34 - 1.47: 2720 1.47 - 1.59: 4755 1.59 - 1.71: 0 1.71 - 1.83: 110 Bond restraints: 11022 Sorted by residual: bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG B1015 " pdb=" O5 NAG B1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C1 NAG A1015 " pdb=" O5 NAG A1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 11017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14090 2.04 - 4.08: 679 4.08 - 6.13: 115 6.13 - 8.17: 34 8.17 - 10.21: 4 Bond angle restraints: 14922 Sorted by residual: angle pdb=" C HIS A 1 " pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C HIS B 1 " pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" N ASP A 542 " pdb=" CA ASP A 542 " pdb=" C ASP A 542 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" N ASP B 542 " pdb=" CA ASP B 542 " pdb=" C ASP B 542 " ideal model delta sigma weight residual 109.81 118.46 -8.65 2.21e+00 2.05e-01 1.53e+01 angle pdb=" N ILE A 136 " pdb=" CA ILE A 136 " pdb=" C ILE A 136 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 ... (remaining 14917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6778 21.38 - 42.75: 219 42.75 - 64.13: 21 64.13 - 85.51: 22 85.51 - 106.88: 8 Dihedral angle restraints: 7048 sinusoidal: 3298 harmonic: 3750 Sorted by residual: dihedral pdb=" CA CYS A 468 " pdb=" C CYS A 468 " pdb=" N GLU A 469 " pdb=" CA GLU A 469 " ideal model delta harmonic sigma weight residual -180.00 -129.36 -50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA CYS B 468 " pdb=" C CYS B 468 " pdb=" N GLU B 469 " pdb=" CA GLU B 469 " ideal model delta harmonic sigma weight residual -180.00 -129.40 -50.60 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL M 715 " pdb=" C VAL M 715 " pdb=" N PRO M 716 " pdb=" CA PRO M 716 " ideal model delta harmonic sigma weight residual 180.00 139.05 40.95 0 5.00e+00 4.00e-02 6.71e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1499 0.088 - 0.175: 208 0.175 - 0.263: 5 0.263 - 0.351: 4 0.351 - 0.439: 4 Chirality restraints: 1720 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 397 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 418 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 418 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 1717 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 715 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO P 716 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 716 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO P 716 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 715 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO M 716 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO M 716 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO M 716 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 715 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C VAL P 715 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL P 715 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO P 716 " -0.017 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3339 2.83 - 3.35: 9921 3.35 - 3.87: 18724 3.87 - 4.38: 20091 4.38 - 4.90: 33375 Nonbonded interactions: 85450 Sorted by model distance: nonbonded pdb=" O SER B 323 " pdb=" OG SER B 326 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 323 " pdb=" OG SER A 326 " model vdw 2.314 3.040 nonbonded pdb=" O CYS K 7 " pdb=" ND1 HIS L 5 " model vdw 2.314 3.120 nonbonded pdb=" O PRO A 558 " pdb=" OG1 THR A 560 " model vdw 2.314 3.040 nonbonded pdb=" O PRO B 558 " pdb=" OG1 THR B 560 " model vdw 2.314 3.040 ... (remaining 85445 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'M' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.008 0.067 11080 Z= 0.379 Angle : 1.096 11.131 15066 Z= 0.558 Chirality : 0.061 0.439 1720 Planarity : 0.007 0.111 1876 Dihedral : 11.758 106.882 4534 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.60 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.66 % 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: -3.39 (0.21), residues: 1254 helix: -2.50 (0.29), residues: 170 sheet: -0.51 (0.45), residues: 132 loop : -2.69 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 181 TYR 0.028 0.004 TYR N 19 PHE 0.046 0.004 PHE M 714 TRP 0.023 0.003 TRP A 251 HIS 0.015 0.003 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00783 (11022) covalent geometry : angle 1.05867 (14922) SS BOND : bond 0.00459 ( 30) SS BOND : angle 1.40484 ( 60) hydrogen bonds : bond 0.23962 ( 226) hydrogen bonds : angle 10.82059 ( 588) link_BETA1-4 : bond 0.00654 ( 10) link_BETA1-4 : angle 3.44492 ( 30) link_BETA1-6 : bond 0.00473 ( 6) link_BETA1-6 : angle 2.44403 ( 18) link_NAG-ASN : bond 0.00484 ( 12) link_NAG-ASN : angle 4.71706 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9351 (mt0) cc_final: 0.9116 (mt0) REVERT: A 109 LEU cc_start: 0.9720 (tp) cc_final: 0.9497 (tp) REVERT: A 120 GLU cc_start: 0.9301 (tt0) cc_final: 0.9051 (tp30) REVERT: A 294 MET cc_start: 0.8546 (ppp) cc_final: 0.8067 (ppp) REVERT: A 322 ASP cc_start: 0.9403 (p0) cc_final: 0.9087 (p0) REVERT: A 442 MET cc_start: 0.9688 (ttt) cc_final: 0.9083 (tpt) REVERT: A 479 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8029 (ttp80) REVERT: A 480 THR cc_start: 0.8542 (p) cc_final: 0.8252 (t) REVERT: A 485 ILE cc_start: 0.9686 (mt) cc_final: 0.9464 (mm) REVERT: A 486 LEU cc_start: 0.9637 (tp) cc_final: 0.8914 (mt) REVERT: A 487 LEU cc_start: 0.9776 (mt) cc_final: 0.9453 (mm) REVERT: A 551 TRP cc_start: 0.9413 (t-100) cc_final: 0.8728 (t-100) REVERT: B 109 LEU cc_start: 0.9701 (tp) cc_final: 0.9386 (tp) REVERT: B 110 MET cc_start: 0.8619 (mmt) cc_final: 0.8336 (mmm) REVERT: B 178 PHE cc_start: 0.8918 (m-10) cc_final: 0.8592 (p90) REVERT: B 294 MET cc_start: 0.8709 (ppp) cc_final: 0.8201 (ppp) REVERT: B 322 ASP cc_start: 0.9462 (p0) cc_final: 0.9047 (p0) REVERT: B 376 LEU cc_start: 0.9377 (mt) cc_final: 0.9173 (tp) REVERT: B 442 MET cc_start: 0.9712 (ttt) cc_final: 0.9087 (tpt) REVERT: B 479 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8164 (ttp80) REVERT: B 486 LEU cc_start: 0.9658 (tp) cc_final: 0.9076 (mt) REVERT: B 487 LEU cc_start: 0.9722 (mt) cc_final: 0.9341 (mm) REVERT: L 11 LEU cc_start: 0.9625 (tp) cc_final: 0.9327 (tp) REVERT: L 18 VAL cc_start: 0.9290 (t) cc_final: 0.9038 (p) REVERT: P 697 GLU cc_start: 0.9193 (tt0) cc_final: 0.8752 (pt0) REVERT: P 707 ASP cc_start: 0.9202 (t70) cc_final: 0.8512 (t70) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1176 time to fit residues: 29.5144 Evaluate side-chains 101 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 100 HIS A 187 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 410 GLN A 417 HIS B 1 HIS B 100 HIS B 187 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 410 GLN K 18 ASN ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.047032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035434 restraints weight = 65497.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036833 restraints weight = 43176.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037842 restraints weight = 31809.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038589 restraints weight = 25325.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039155 restraints weight = 21327.232| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11080 Z= 0.181 Angle : 0.786 7.009 15066 Z= 0.390 Chirality : 0.049 0.236 1720 Planarity : 0.006 0.073 1876 Dihedral : 10.428 77.259 2000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.09 % Allowed : 1.28 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.50 % 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: -2.74 (0.23), residues: 1254 helix: -1.28 (0.34), residues: 182 sheet: -0.33 (0.39), residues: 154 loop : -2.40 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 554 TYR 0.028 0.002 TYR K 19 PHE 0.021 0.002 PHE P 714 TRP 0.013 0.002 TRP B 551 HIS 0.004 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00378 (11022) covalent geometry : angle 0.75817 (14922) SS BOND : bond 0.00290 ( 30) SS BOND : angle 1.26065 ( 60) hydrogen bonds : bond 0.05778 ( 226) hydrogen bonds : angle 8.21168 ( 588) link_BETA1-4 : bond 0.00390 ( 10) link_BETA1-4 : angle 2.50820 ( 30) link_BETA1-6 : bond 0.00417 ( 6) link_BETA1-6 : angle 1.58921 ( 18) link_NAG-ASN : bond 0.00440 ( 12) link_NAG-ASN : angle 3.28926 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9339 (mt0) cc_final: 0.9062 (mt0) REVERT: A 81 VAL cc_start: 0.9677 (t) cc_final: 0.9229 (t) REVERT: A 98 MET cc_start: 0.8613 (tpp) cc_final: 0.8171 (mmm) REVERT: A 101 LEU cc_start: 0.9804 (tp) cc_final: 0.9573 (mt) REVERT: A 109 LEU cc_start: 0.9730 (tp) cc_final: 0.9494 (tp) REVERT: A 110 MET cc_start: 0.8513 (mmp) cc_final: 0.8055 (mmm) REVERT: A 120 GLU cc_start: 0.9312 (tt0) cc_final: 0.8896 (tt0) REVERT: A 294 MET cc_start: 0.8644 (ppp) cc_final: 0.8096 (ppp) REVERT: A 322 ASP cc_start: 0.9338 (p0) cc_final: 0.9017 (p0) REVERT: A 442 MET cc_start: 0.9556 (ttt) cc_final: 0.8967 (tpt) REVERT: A 551 TRP cc_start: 0.9313 (t-100) cc_final: 0.8830 (t-100) REVERT: B 54 LEU cc_start: 0.9403 (tp) cc_final: 0.9122 (tp) REVERT: B 81 VAL cc_start: 0.9630 (t) cc_final: 0.9425 (t) REVERT: B 109 LEU cc_start: 0.9624 (tp) cc_final: 0.9249 (tp) REVERT: B 110 MET cc_start: 0.8487 (mmt) cc_final: 0.8217 (mmm) REVERT: B 125 LEU cc_start: 0.9614 (tp) cc_final: 0.9272 (tp) REVERT: B 294 MET cc_start: 0.8611 (ppp) cc_final: 0.8065 (ppp) REVERT: B 322 ASP cc_start: 0.9383 (p0) cc_final: 0.8968 (p0) REVERT: B 442 MET cc_start: 0.9570 (ttt) cc_final: 0.9014 (tpt) REVERT: B 504 MET cc_start: 0.8918 (mmp) cc_final: 0.8559 (tpp) REVERT: M 703 LYS cc_start: 0.9407 (tptm) cc_final: 0.9146 (tptm) REVERT: M 706 GLU cc_start: 0.9101 (tp30) cc_final: 0.8841 (tp30) REVERT: P 697 GLU cc_start: 0.9160 (tt0) cc_final: 0.8231 (pp20) REVERT: P 706 GLU cc_start: 0.9196 (tp30) cc_final: 0.8573 (tp30) REVERT: P 720 ARG cc_start: 0.5593 (mmp80) cc_final: 0.3541 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0996 time to fit residues: 19.5052 Evaluate side-chains 93 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 0.0570 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS O 10 HIS P 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035647 restraints weight = 64455.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037028 restraints weight = 42634.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038080 restraints weight = 31503.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038850 restraints weight = 25059.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.039435 restraints weight = 21029.227| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11080 Z= 0.135 Angle : 0.713 8.515 15066 Z= 0.353 Chirality : 0.047 0.238 1720 Planarity : 0.005 0.062 1876 Dihedral : 8.942 76.698 2000 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.46 (0.23), residues: 1254 helix: -0.86 (0.36), residues: 178 sheet: -0.35 (0.39), residues: 158 loop : -2.20 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.024 0.001 TYR K 19 PHE 0.017 0.002 PHE P 714 TRP 0.009 0.001 TRP B 551 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00288 (11022) covalent geometry : angle 0.67958 (14922) SS BOND : bond 0.00238 ( 30) SS BOND : angle 1.86569 ( 60) hydrogen bonds : bond 0.04457 ( 226) hydrogen bonds : angle 7.38310 ( 588) link_BETA1-4 : bond 0.00412 ( 10) link_BETA1-4 : angle 2.43530 ( 30) link_BETA1-6 : bond 0.00465 ( 6) link_BETA1-6 : angle 1.44837 ( 18) link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 3.06157 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9329 (mt0) cc_final: 0.9054 (mt0) REVERT: A 81 VAL cc_start: 0.9618 (t) cc_final: 0.9303 (t) REVERT: A 98 MET cc_start: 0.8600 (tpp) cc_final: 0.8052 (mmt) REVERT: A 101 LEU cc_start: 0.9800 (tp) cc_final: 0.9535 (mt) REVERT: A 110 MET cc_start: 0.8544 (mmp) cc_final: 0.8135 (mmm) REVERT: A 294 MET cc_start: 0.8350 (ppp) cc_final: 0.7744 (ppp) REVERT: A 322 ASP cc_start: 0.9286 (p0) cc_final: 0.8946 (p0) REVERT: A 442 MET cc_start: 0.9566 (ttt) cc_final: 0.9075 (tpt) REVERT: A 504 MET cc_start: 0.9057 (tpt) cc_final: 0.8844 (tpt) REVERT: A 551 TRP cc_start: 0.9281 (t-100) cc_final: 0.8857 (t-100) REVERT: B 34 GLN cc_start: 0.9524 (mt0) cc_final: 0.9293 (mt0) REVERT: B 54 LEU cc_start: 0.9415 (tp) cc_final: 0.9138 (tp) REVERT: B 109 LEU cc_start: 0.9624 (tp) cc_final: 0.9422 (tp) REVERT: B 294 MET cc_start: 0.8532 (ppp) cc_final: 0.7990 (ppp) REVERT: B 322 ASP cc_start: 0.9331 (p0) cc_final: 0.8928 (p0) REVERT: B 442 MET cc_start: 0.9573 (ttt) cc_final: 0.8947 (tpt) REVERT: B 553 MET cc_start: 0.8853 (tpp) cc_final: 0.8473 (tpp) REVERT: M 703 LYS cc_start: 0.9386 (tptm) cc_final: 0.9064 (tptm) REVERT: M 706 GLU cc_start: 0.9229 (tp30) cc_final: 0.8746 (tp30) REVERT: P 697 GLU cc_start: 0.9123 (tt0) cc_final: 0.8280 (pp20) REVERT: P 706 GLU cc_start: 0.9306 (tp30) cc_final: 0.8934 (tp30) REVERT: P 720 ARG cc_start: 0.5820 (mmp80) cc_final: 0.3726 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1111 time to fit residues: 18.8036 Evaluate side-chains 88 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.047301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.035363 restraints weight = 63532.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036746 restraints weight = 42159.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037718 restraints weight = 31315.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.038526 restraints weight = 25291.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039145 restraints weight = 21152.977| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11080 Z= 0.119 Angle : 0.673 6.650 15066 Z= 0.332 Chirality : 0.046 0.235 1720 Planarity : 0.004 0.057 1876 Dihedral : 8.035 74.806 2000 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.32 (0.24), residues: 1254 helix: -0.93 (0.36), residues: 178 sheet: -0.63 (0.36), residues: 176 loop : -2.00 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 498 TYR 0.023 0.001 TYR N 19 PHE 0.013 0.001 PHE B 382 TRP 0.007 0.001 TRP B 551 HIS 0.006 0.001 HIS O 10 Details of bonding type rmsd covalent geometry : bond 0.00260 (11022) covalent geometry : angle 0.64646 (14922) SS BOND : bond 0.00264 ( 30) SS BOND : angle 1.19138 ( 60) hydrogen bonds : bond 0.04046 ( 226) hydrogen bonds : angle 6.95459 ( 588) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 2.36845 ( 30) link_BETA1-6 : bond 0.00384 ( 6) link_BETA1-6 : angle 1.38201 ( 18) link_NAG-ASN : bond 0.00369 ( 12) link_NAG-ASN : angle 2.87876 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9197 (mt0) cc_final: 0.8930 (mt0) REVERT: A 81 VAL cc_start: 0.9610 (t) cc_final: 0.9273 (t) REVERT: A 98 MET cc_start: 0.8663 (tpp) cc_final: 0.8358 (mmm) REVERT: A 101 LEU cc_start: 0.9791 (tp) cc_final: 0.9519 (mt) REVERT: A 109 LEU cc_start: 0.9754 (tp) cc_final: 0.9544 (tp) REVERT: A 110 MET cc_start: 0.8550 (mmp) cc_final: 0.8105 (mmm) REVERT: A 294 MET cc_start: 0.8372 (ppp) cc_final: 0.7794 (ppp) REVERT: A 322 ASP cc_start: 0.9264 (p0) cc_final: 0.8914 (p0) REVERT: A 442 MET cc_start: 0.9533 (ttt) cc_final: 0.9059 (tpt) REVERT: A 551 TRP cc_start: 0.9271 (t-100) cc_final: 0.8886 (t-100) REVERT: B 54 LEU cc_start: 0.9410 (tp) cc_final: 0.9145 (tp) REVERT: B 294 MET cc_start: 0.8562 (ppp) cc_final: 0.8036 (ppp) REVERT: B 322 ASP cc_start: 0.9323 (p0) cc_final: 0.8881 (p0) REVERT: B 357 ASN cc_start: 0.8792 (p0) cc_final: 0.8591 (t0) REVERT: B 442 MET cc_start: 0.9556 (ttt) cc_final: 0.9037 (tpt) REVERT: B 486 LEU cc_start: 0.9618 (tp) cc_final: 0.9393 (tp) REVERT: B 504 MET cc_start: 0.9310 (mmp) cc_final: 0.9107 (mmm) REVERT: B 553 MET cc_start: 0.8833 (tpp) cc_final: 0.8455 (tpp) REVERT: M 703 LYS cc_start: 0.9411 (tptm) cc_final: 0.9074 (tptm) REVERT: M 706 GLU cc_start: 0.9187 (tp30) cc_final: 0.8636 (tp30) REVERT: P 697 GLU cc_start: 0.9111 (tt0) cc_final: 0.8308 (pp20) REVERT: P 706 GLU cc_start: 0.9341 (tp30) cc_final: 0.8966 (tp30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0955 time to fit residues: 15.7513 Evaluate side-chains 89 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.0570 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 32 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN L 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033442 restraints weight = 66788.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.034693 restraints weight = 44749.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.035631 restraints weight = 33493.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.036321 restraints weight = 26953.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036811 restraints weight = 22858.193| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11080 Z= 0.252 Angle : 0.793 6.751 15066 Z= 0.384 Chirality : 0.047 0.221 1720 Planarity : 0.005 0.061 1876 Dihedral : 7.947 73.765 2000 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.43 (0.23), residues: 1254 helix: -1.39 (0.35), residues: 178 sheet: -0.50 (0.36), residues: 176 loop : -2.03 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 554 TYR 0.030 0.002 TYR N 19 PHE 0.062 0.002 PHE P 714 TRP 0.017 0.002 TRP A 551 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00535 (11022) covalent geometry : angle 0.77137 (14922) SS BOND : bond 0.00292 ( 30) SS BOND : angle 1.10912 ( 60) hydrogen bonds : bond 0.04348 ( 226) hydrogen bonds : angle 7.15771 ( 588) link_BETA1-4 : bond 0.00387 ( 10) link_BETA1-4 : angle 2.30982 ( 30) link_BETA1-6 : bond 0.00315 ( 6) link_BETA1-6 : angle 1.57073 ( 18) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 2.93902 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9234 (mt0) cc_final: 0.8934 (mt0) REVERT: A 81 VAL cc_start: 0.9643 (t) cc_final: 0.9280 (t) REVERT: A 109 LEU cc_start: 0.9755 (tp) cc_final: 0.9451 (tp) REVERT: A 110 MET cc_start: 0.8623 (mmp) cc_final: 0.8170 (mmm) REVERT: A 294 MET cc_start: 0.8327 (ppp) cc_final: 0.7822 (ppp) REVERT: A 322 ASP cc_start: 0.9263 (p0) cc_final: 0.8936 (p0) REVERT: A 442 MET cc_start: 0.9596 (ttt) cc_final: 0.9238 (tmm) REVERT: A 479 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7810 (ttp80) REVERT: A 486 LEU cc_start: 0.9691 (tp) cc_final: 0.9027 (tp) REVERT: A 504 MET cc_start: 0.9012 (mmm) cc_final: 0.8809 (mmm) REVERT: A 551 TRP cc_start: 0.9435 (t-100) cc_final: 0.8942 (t-100) REVERT: A 553 MET cc_start: 0.9163 (tpt) cc_final: 0.8954 (tpt) REVERT: B 54 LEU cc_start: 0.9497 (tp) cc_final: 0.9257 (tp) REVERT: B 294 MET cc_start: 0.8583 (ppp) cc_final: 0.8133 (ppp) REVERT: B 322 ASP cc_start: 0.9330 (p0) cc_final: 0.9006 (p0) REVERT: B 442 MET cc_start: 0.9602 (ttt) cc_final: 0.9094 (tpt) REVERT: B 479 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7960 (ttp80) REVERT: B 486 LEU cc_start: 0.9681 (tp) cc_final: 0.8908 (mt) REVERT: B 504 MET cc_start: 0.9288 (mmp) cc_final: 0.8936 (mmm) REVERT: B 553 MET cc_start: 0.8941 (tpp) cc_final: 0.8598 (tpp) REVERT: M 695 GLU cc_start: 0.9032 (mp0) cc_final: 0.8755 (mp0) REVERT: M 703 LYS cc_start: 0.9440 (tptm) cc_final: 0.9104 (tptm) REVERT: M 706 GLU cc_start: 0.9237 (tp30) cc_final: 0.8660 (tp30) REVERT: O 13 GLU cc_start: 0.9073 (mp0) cc_final: 0.8806 (mp0) REVERT: P 703 LYS cc_start: 0.9430 (tptm) cc_final: 0.9102 (tptm) REVERT: P 706 GLU cc_start: 0.9403 (tp30) cc_final: 0.8923 (tp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0986 time to fit residues: 15.4441 Evaluate side-chains 81 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 62 optimal weight: 0.0010 chunk 87 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.034748 restraints weight = 65000.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036080 restraints weight = 42767.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037061 restraints weight = 31547.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037745 restraints weight = 25279.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038359 restraints weight = 21567.940| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11080 Z= 0.127 Angle : 0.680 6.628 15066 Z= 0.336 Chirality : 0.046 0.234 1720 Planarity : 0.004 0.059 1876 Dihedral : 7.603 71.048 2000 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.26 (0.24), residues: 1254 helix: -1.23 (0.36), residues: 176 sheet: -0.46 (0.35), residues: 176 loop : -1.91 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.028 0.002 TYR K 19 PHE 0.054 0.002 PHE M 714 TRP 0.011 0.001 TRP A 551 HIS 0.003 0.001 HIS O 10 Details of bonding type rmsd covalent geometry : bond 0.00274 (11022) covalent geometry : angle 0.65520 (14922) SS BOND : bond 0.00399 ( 30) SS BOND : angle 1.26823 ( 60) hydrogen bonds : bond 0.03975 ( 226) hydrogen bonds : angle 6.80215 ( 588) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 2.13291 ( 30) link_BETA1-6 : bond 0.00375 ( 6) link_BETA1-6 : angle 1.41848 ( 18) link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.87483 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9274 (mt0) cc_final: 0.8992 (mt0) REVERT: A 81 VAL cc_start: 0.9621 (t) cc_final: 0.9250 (t) REVERT: A 109 LEU cc_start: 0.9759 (tp) cc_final: 0.9556 (tp) REVERT: A 110 MET cc_start: 0.8565 (mmp) cc_final: 0.8245 (mmm) REVERT: A 322 ASP cc_start: 0.9162 (p0) cc_final: 0.8817 (p0) REVERT: A 442 MET cc_start: 0.9573 (ttt) cc_final: 0.9154 (tmm) REVERT: A 479 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7840 (ttp80) REVERT: A 486 LEU cc_start: 0.9681 (tp) cc_final: 0.8988 (tp) REVERT: A 504 MET cc_start: 0.9066 (mmm) cc_final: 0.8848 (mmm) REVERT: A 551 TRP cc_start: 0.9347 (t-100) cc_final: 0.8858 (t-100) REVERT: B 34 GLN cc_start: 0.9383 (mt0) cc_final: 0.9070 (mt0) REVERT: B 38 MET cc_start: 0.8647 (mtt) cc_final: 0.8422 (mtt) REVERT: B 54 LEU cc_start: 0.9492 (tp) cc_final: 0.9243 (tp) REVERT: B 101 LEU cc_start: 0.9673 (mt) cc_final: 0.9348 (mm) REVERT: B 109 LEU cc_start: 0.9650 (tp) cc_final: 0.9450 (tp) REVERT: B 442 MET cc_start: 0.9553 (ttt) cc_final: 0.9034 (tpt) REVERT: B 479 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7976 (ttp80) REVERT: B 486 LEU cc_start: 0.9664 (tp) cc_final: 0.8917 (tp) REVERT: B 504 MET cc_start: 0.9338 (mmp) cc_final: 0.8960 (mmm) REVERT: B 553 MET cc_start: 0.8950 (tpp) cc_final: 0.8617 (tpp) REVERT: M 695 GLU cc_start: 0.9104 (mp0) cc_final: 0.8842 (mp0) REVERT: M 703 LYS cc_start: 0.9412 (tptm) cc_final: 0.9061 (tptm) REVERT: M 706 GLU cc_start: 0.9200 (tp30) cc_final: 0.8570 (tp30) REVERT: P 703 LYS cc_start: 0.9389 (tptm) cc_final: 0.9045 (tptm) REVERT: P 706 GLU cc_start: 0.9454 (tp30) cc_final: 0.8930 (tp30) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0940 time to fit residues: 15.2447 Evaluate side-chains 79 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.035275 restraints weight = 63011.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036618 restraints weight = 41581.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037638 restraints weight = 30894.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038385 restraints weight = 24576.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038965 restraints weight = 20678.543| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11080 Z= 0.106 Angle : 0.671 13.011 15066 Z= 0.326 Chirality : 0.047 0.232 1720 Planarity : 0.004 0.053 1876 Dihedral : 7.763 79.408 2000 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.10 (0.24), residues: 1254 helix: -0.96 (0.38), residues: 178 sheet: -0.38 (0.35), residues: 176 loop : -1.83 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.023 0.001 TYR N 19 PHE 0.039 0.002 PHE M 714 TRP 0.009 0.001 TRP A 551 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00230 (11022) covalent geometry : angle 0.64958 (14922) SS BOND : bond 0.00355 ( 30) SS BOND : angle 1.01101 ( 60) hydrogen bonds : bond 0.03773 ( 226) hydrogen bonds : angle 6.56173 ( 588) link_BETA1-4 : bond 0.00442 ( 10) link_BETA1-4 : angle 2.06004 ( 30) link_BETA1-6 : bond 0.00401 ( 6) link_BETA1-6 : angle 1.31633 ( 18) link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 2.70715 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9225 (mt0) cc_final: 0.8901 (mt0) REVERT: A 81 VAL cc_start: 0.9593 (t) cc_final: 0.9227 (t) REVERT: A 87 LEU cc_start: 0.9116 (mt) cc_final: 0.8876 (tp) REVERT: A 109 LEU cc_start: 0.9742 (tp) cc_final: 0.9517 (tp) REVERT: A 110 MET cc_start: 0.8425 (mmp) cc_final: 0.8146 (mmm) REVERT: A 322 ASP cc_start: 0.9156 (p0) cc_final: 0.8757 (p0) REVERT: A 357 ASN cc_start: 0.8815 (p0) cc_final: 0.8546 (t0) REVERT: A 442 MET cc_start: 0.9545 (ttt) cc_final: 0.9076 (tmm) REVERT: A 486 LEU cc_start: 0.9650 (tp) cc_final: 0.8942 (tp) REVERT: A 504 MET cc_start: 0.9069 (mmm) cc_final: 0.8815 (mmm) REVERT: A 551 TRP cc_start: 0.9295 (t-100) cc_final: 0.8816 (t-100) REVERT: B 34 GLN cc_start: 0.9291 (mt0) cc_final: 0.8963 (mt0) REVERT: B 54 LEU cc_start: 0.9448 (tp) cc_final: 0.9243 (tp) REVERT: B 101 LEU cc_start: 0.9666 (mt) cc_final: 0.9334 (mm) REVERT: B 150 ASP cc_start: 0.8372 (m-30) cc_final: 0.7816 (p0) REVERT: B 442 MET cc_start: 0.9522 (ttt) cc_final: 0.9021 (tpt) REVERT: B 473 LEU cc_start: 0.9109 (mt) cc_final: 0.8906 (mt) REVERT: B 486 LEU cc_start: 0.9637 (tp) cc_final: 0.9435 (tp) REVERT: B 504 MET cc_start: 0.9354 (mmp) cc_final: 0.9139 (mmm) REVERT: B 553 MET cc_start: 0.8906 (tpp) cc_final: 0.8513 (tpp) REVERT: M 695 GLU cc_start: 0.9067 (mp0) cc_final: 0.8815 (mp0) REVERT: M 703 LYS cc_start: 0.9400 (tptm) cc_final: 0.9050 (tptm) REVERT: M 706 GLU cc_start: 0.9173 (tp30) cc_final: 0.8531 (tp30) REVERT: L 13 GLU cc_start: 0.9189 (mp0) cc_final: 0.8900 (mp0) REVERT: P 695 GLU cc_start: 0.9094 (mp0) cc_final: 0.8865 (mp0) REVERT: P 703 LYS cc_start: 0.9368 (tptm) cc_final: 0.9048 (tptm) REVERT: P 706 GLU cc_start: 0.9422 (tp30) cc_final: 0.8923 (tp30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0892 time to fit residues: 14.8924 Evaluate side-chains 84 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.0270 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.0370 chunk 94 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035590 restraints weight = 63366.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.036915 restraints weight = 41836.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.037933 restraints weight = 31205.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038709 restraints weight = 24869.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039285 restraints weight = 20901.938| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11080 Z= 0.104 Angle : 0.691 11.855 15066 Z= 0.331 Chirality : 0.046 0.227 1720 Planarity : 0.004 0.053 1876 Dihedral : 7.867 73.301 2000 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.06 (0.24), residues: 1254 helix: -0.89 (0.38), residues: 176 sheet: -0.29 (0.36), residues: 176 loop : -1.82 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 479 TYR 0.021 0.001 TYR N 19 PHE 0.029 0.001 PHE M 714 TRP 0.008 0.001 TRP A 551 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00231 (11022) covalent geometry : angle 0.66388 (14922) SS BOND : bond 0.00265 ( 30) SS BOND : angle 1.03255 ( 60) hydrogen bonds : bond 0.03673 ( 226) hydrogen bonds : angle 6.39422 ( 588) link_BETA1-4 : bond 0.00451 ( 10) link_BETA1-4 : angle 2.00407 ( 30) link_BETA1-6 : bond 0.00592 ( 6) link_BETA1-6 : angle 1.23593 ( 18) link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 3.31705 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9236 (mt0) cc_final: 0.8931 (mt0) REVERT: A 81 VAL cc_start: 0.9585 (t) cc_final: 0.9165 (t) REVERT: A 87 LEU cc_start: 0.9101 (mt) cc_final: 0.8870 (tp) REVERT: A 109 LEU cc_start: 0.9746 (tp) cc_final: 0.9444 (tp) REVERT: A 110 MET cc_start: 0.8454 (mmp) cc_final: 0.8040 (mmm) REVERT: A 322 ASP cc_start: 0.9160 (p0) cc_final: 0.8760 (p0) REVERT: A 357 ASN cc_start: 0.8726 (p0) cc_final: 0.8485 (t0) REVERT: A 442 MET cc_start: 0.9504 (ttt) cc_final: 0.9063 (tmm) REVERT: A 473 LEU cc_start: 0.9223 (mt) cc_final: 0.9019 (mt) REVERT: A 504 MET cc_start: 0.8968 (mmm) cc_final: 0.8714 (mmm) REVERT: A 553 MET cc_start: 0.8902 (tpt) cc_final: 0.8657 (tpp) REVERT: B 34 GLN cc_start: 0.9290 (mt0) cc_final: 0.8980 (mt0) REVERT: B 150 ASP cc_start: 0.8438 (m-30) cc_final: 0.7849 (p0) REVERT: B 442 MET cc_start: 0.9513 (ttt) cc_final: 0.9023 (tpt) REVERT: B 486 LEU cc_start: 0.9615 (tp) cc_final: 0.9400 (tp) REVERT: B 504 MET cc_start: 0.9293 (mmp) cc_final: 0.8973 (mmm) REVERT: B 553 MET cc_start: 0.8943 (tpp) cc_final: 0.8619 (tpp) REVERT: M 695 GLU cc_start: 0.9116 (mp0) cc_final: 0.8893 (mp0) REVERT: M 703 LYS cc_start: 0.9420 (tptm) cc_final: 0.9078 (tptm) REVERT: M 706 GLU cc_start: 0.9152 (tp30) cc_final: 0.8509 (tp30) REVERT: P 703 LYS cc_start: 0.9371 (tptm) cc_final: 0.9052 (tptm) REVERT: P 706 GLU cc_start: 0.9427 (tp30) cc_final: 0.8861 (tp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0941 time to fit residues: 14.8499 Evaluate side-chains 86 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.045283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033721 restraints weight = 65459.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.035029 restraints weight = 43183.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035995 restraints weight = 31965.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036702 restraints weight = 25585.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.037238 restraints weight = 21593.393| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11080 Z= 0.230 Angle : 0.776 11.172 15066 Z= 0.374 Chirality : 0.047 0.216 1720 Planarity : 0.005 0.057 1876 Dihedral : 8.288 90.799 2000 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.18 (0.24), residues: 1254 helix: -1.31 (0.35), residues: 176 sheet: -0.26 (0.37), residues: 172 loop : -1.85 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 479 TYR 0.025 0.002 TYR K 14 PHE 0.039 0.002 PHE M 714 TRP 0.017 0.002 TRP A 551 HIS 0.006 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00491 (11022) covalent geometry : angle 0.75682 (14922) SS BOND : bond 0.00305 ( 30) SS BOND : angle 1.31572 ( 60) hydrogen bonds : bond 0.03852 ( 226) hydrogen bonds : angle 6.69265 ( 588) link_BETA1-4 : bond 0.00373 ( 10) link_BETA1-4 : angle 2.06012 ( 30) link_BETA1-6 : bond 0.00451 ( 6) link_BETA1-6 : angle 1.44073 ( 18) link_NAG-ASN : bond 0.00304 ( 12) link_NAG-ASN : angle 2.70070 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9227 (mt0) cc_final: 0.8877 (mt0) REVERT: A 81 VAL cc_start: 0.9656 (t) cc_final: 0.9185 (t) REVERT: A 109 LEU cc_start: 0.9763 (tp) cc_final: 0.9418 (tp) REVERT: A 110 MET cc_start: 0.8480 (mmp) cc_final: 0.8101 (mmm) REVERT: A 322 ASP cc_start: 0.9204 (p0) cc_final: 0.8837 (p0) REVERT: A 442 MET cc_start: 0.9560 (ttt) cc_final: 0.9222 (tmm) REVERT: A 504 MET cc_start: 0.8939 (mmm) cc_final: 0.8700 (mmm) REVERT: B 81 VAL cc_start: 0.9617 (t) cc_final: 0.9353 (t) REVERT: B 442 MET cc_start: 0.9590 (ttt) cc_final: 0.9130 (tpt) REVERT: B 479 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7842 (ttp80) REVERT: B 486 LEU cc_start: 0.9683 (tp) cc_final: 0.8940 (mt) REVERT: B 504 MET cc_start: 0.9225 (mmp) cc_final: 0.8864 (mmm) REVERT: B 553 MET cc_start: 0.8987 (tpp) cc_final: 0.8673 (tpp) REVERT: M 695 GLU cc_start: 0.9137 (mp0) cc_final: 0.8904 (mp0) REVERT: M 703 LYS cc_start: 0.9422 (tptm) cc_final: 0.9106 (tptm) REVERT: M 706 GLU cc_start: 0.9331 (tp30) cc_final: 0.8938 (tp30) REVERT: L 13 GLU cc_start: 0.9148 (mp0) cc_final: 0.8886 (mp0) REVERT: P 693 LEU cc_start: 0.9527 (mp) cc_final: 0.9305 (pt) REVERT: P 703 LYS cc_start: 0.9405 (tptm) cc_final: 0.9107 (tptm) REVERT: P 706 GLU cc_start: 0.9442 (tp30) cc_final: 0.9238 (tp30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0883 time to fit residues: 12.9846 Evaluate side-chains 78 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 0.0000 chunk 83 optimal weight: 0.0170 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035618 restraints weight = 63088.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037009 restraints weight = 41635.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.038051 restraints weight = 30796.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.038809 restraints weight = 24565.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039368 restraints weight = 20656.741| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11080 Z= 0.103 Angle : 0.692 11.896 15066 Z= 0.332 Chirality : 0.047 0.226 1720 Planarity : 0.004 0.056 1876 Dihedral : 7.613 84.641 2000 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.04 (0.24), residues: 1254 helix: -1.04 (0.38), residues: 174 sheet: -0.20 (0.37), residues: 174 loop : -1.78 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 479 TYR 0.020 0.001 TYR N 19 PHE 0.023 0.001 PHE M 714 TRP 0.014 0.001 TRP A 551 HIS 0.004 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00222 (11022) covalent geometry : angle 0.67215 (14922) SS BOND : bond 0.00277 ( 30) SS BOND : angle 1.02652 ( 60) hydrogen bonds : bond 0.03612 ( 226) hydrogen bonds : angle 6.23512 ( 588) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 1.88363 ( 30) link_BETA1-6 : bond 0.00642 ( 6) link_BETA1-6 : angle 1.19821 ( 18) link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 2.75452 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9298 (mt0) cc_final: 0.9064 (mt0) REVERT: A 81 VAL cc_start: 0.9600 (t) cc_final: 0.9138 (t) REVERT: A 87 LEU cc_start: 0.9107 (mt) cc_final: 0.8863 (tp) REVERT: A 108 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.8720 (m-40) REVERT: A 109 LEU cc_start: 0.9760 (tp) cc_final: 0.9414 (tp) REVERT: A 110 MET cc_start: 0.8342 (mmp) cc_final: 0.7954 (mmm) REVERT: A 442 MET cc_start: 0.9530 (ttt) cc_final: 0.9146 (tmm) REVERT: A 504 MET cc_start: 0.8976 (mmm) cc_final: 0.8744 (mmm) REVERT: B 34 GLN cc_start: 0.9322 (mt0) cc_final: 0.9039 (mt0) REVERT: B 54 LEU cc_start: 0.9490 (tp) cc_final: 0.9285 (tp) REVERT: B 87 LEU cc_start: 0.9089 (mt) cc_final: 0.8847 (tp) REVERT: B 150 ASP cc_start: 0.8487 (m-30) cc_final: 0.8072 (p0) REVERT: B 442 MET cc_start: 0.9538 (ttt) cc_final: 0.9084 (tpt) REVERT: B 486 LEU cc_start: 0.9628 (tp) cc_final: 0.8874 (mt) REVERT: B 504 MET cc_start: 0.9243 (mmp) cc_final: 0.8898 (mmm) REVERT: B 552 LEU cc_start: 0.9549 (tp) cc_final: 0.9296 (tp) REVERT: B 553 MET cc_start: 0.8932 (tpp) cc_final: 0.8665 (tpp) REVERT: M 695 GLU cc_start: 0.9148 (mp0) cc_final: 0.8908 (mp0) REVERT: M 706 GLU cc_start: 0.9326 (tp30) cc_final: 0.8880 (tp30) REVERT: L 13 GLU cc_start: 0.9183 (mp0) cc_final: 0.8900 (mp0) REVERT: P 693 LEU cc_start: 0.9510 (mp) cc_final: 0.9225 (pt) REVERT: P 703 LYS cc_start: 0.9360 (tptm) cc_final: 0.9052 (tptm) REVERT: P 706 GLU cc_start: 0.9445 (tp30) cc_final: 0.8855 (tp30) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0914 time to fit residues: 15.1547 Evaluate side-chains 87 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 126 optimal weight: 3.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.035537 restraints weight = 63977.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036893 restraints weight = 42063.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037906 restraints weight = 31186.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038634 restraints weight = 24869.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039192 restraints weight = 20980.308| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11080 Z= 0.115 Angle : 0.681 10.962 15066 Z= 0.328 Chirality : 0.046 0.243 1720 Planarity : 0.004 0.052 1876 Dihedral : 7.225 82.378 2000 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.04 (0.24), residues: 1254 helix: -1.09 (0.38), residues: 174 sheet: -0.04 (0.36), residues: 170 loop : -1.80 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 479 TYR 0.025 0.001 TYR K 14 PHE 0.027 0.001 PHE M 714 TRP 0.011 0.001 TRP B 551 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00256 (11022) covalent geometry : angle 0.65957 (14922) SS BOND : bond 0.00252 ( 30) SS BOND : angle 1.01042 ( 60) hydrogen bonds : bond 0.03393 ( 226) hydrogen bonds : angle 6.27973 ( 588) link_BETA1-4 : bond 0.00400 ( 10) link_BETA1-4 : angle 1.91490 ( 30) link_BETA1-6 : bond 0.00470 ( 6) link_BETA1-6 : angle 1.29846 ( 18) link_NAG-ASN : bond 0.00214 ( 12) link_NAG-ASN : angle 2.84457 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.84 seconds wall clock time: 27 minutes 46.66 seconds (1666.66 seconds total)