Starting phenix.real_space_refine on Fri Sep 11 19:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ce9_7462/09_2026/6ce9_7462.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.11, per 1000 atoms: 0.29 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: 1.24 Conformation dependent library (CDL) restraints added in 453.0 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: 0.48 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: 1.78 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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 - 14.49: 5973 14.49 - 28.98: 363 28.98 - 43.47: 92 43.47 - 57.96: 8 57.96 - 72.45: 10 Dihedral angle restraints: 6446 sinusoidal: 2696 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 6443 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 10.009 70.733 3932 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/Z covalent geometry : bond 0.00783 / 0.38 (11022) covalent geometry : angle 1.05867 / 0.55 (14922) SS BOND : bond 0.00459 / 0.32 ( 30) SS BOND : angle 1.40484 / 0.97 ( 60) hydrogen bonds : bond 0.23962 / 15.85 ( 226) hydrogen bonds : angle 10.82059 / 7.17 ( 588) link_BETA1-4 : bond 0.00654 / 0.49 ( 10) link_BETA1-4 : angle 3.44492 / 2.62 ( 30) link_BETA1-6 : bond 0.00473 / 0.26 ( 6) link_BETA1-6 : angle 2.44403 / 1.77 ( 18) link_NAG-ASN : bond 0.00484 / 0.37 ( 12) link_NAG-ASN : angle 4.71706 / 3.05 ( 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 : 0.411 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: 0.8547 (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: 0.9192 (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: 0.1179 time to fit residues: 30.1535 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 : 0.430 ------------------------------------------------------------------------------- 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... 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 O 10 HIS ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.047026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035448 restraints weight = 65581.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036845 restraints weight = 43091.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037853 restraints weight = 31740.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038611 restraints weight = 25269.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039127 restraints weight = 21228.683| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11080 Z= 0.178 Angle : 0.777 6.930 15066 Z= 0.387 Chirality : 0.049 0.273 1720 Planarity : 0.006 0.073 1876 Dihedral : 7.907 78.022 1398 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.47 % 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: -2.73 (0.23), residues: 1254 helix: -1.26 (0.34), residues: 182 sheet: -0.33 (0.39), residues: 154 loop : -2.39 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 498 TYR 0.028 0.002 TYR K 19 PHE 0.021 0.002 PHE P 714 TRP 0.015 0.002 TRP B 551 HIS 0.004 0.001 HIS A 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (11022) covalent geometry : angle 0.75295 / 0.38 (14922) SS BOND : bond 0.00296 / 0.23 ( 30) SS BOND : angle 1.26746 / 0.80 ( 60) hydrogen bonds : bond 0.05447 / 3.71 ( 226) hydrogen bonds : angle 8.11613 / 5.36 ( 588) link_BETA1-4 : bond 0.00402 / 0.29 ( 10) link_BETA1-4 : angle 2.24522 / 1.67 ( 30) link_BETA1-6 : bond 0.00281 / 0.16 ( 6) link_BETA1-6 : angle 1.49499 / 1.11 ( 18) link_NAG-ASN : bond 0.00430 / 0.34 ( 12) link_NAG-ASN : angle 3.11480 / 1.92 ( 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 136 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.454 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: 0.9332 (mt0) cc_final: 0.9051 (mt0) REVERT: A 75 LEU cc_start: 0.9465 (tp) cc_final: 0.9261 (tp) REVERT: A 81 VAL cc_start: 0.9675 (t) cc_final: 0.9227 (t) REVERT: A 98 MET cc_start: 0.8585 (tpp) cc_final: 0.8148 (mmm) REVERT: A 101 LEU cc_start: 0.9796 (tp) cc_final: 0.9564 (mt) REVERT: A 109 LEU cc_start: 0.9731 (tp) cc_final: 0.9487 (tp) REVERT: A 110 MET cc_start: 0.8527 (mmp) cc_final: 0.8096 (mmm) REVERT: A 120 GLU cc_start: 0.9304 (tt0) cc_final: 0.8892 (tt0) REVERT: A 294 MET cc_start: 0.8648 (ppp) cc_final: 0.8098 (ppp) REVERT: A 322 ASP cc_start: 0.9333 (p0) cc_final: 0.9009 (p0) REVERT: A 442 MET cc_start: 0.9561 (ttt) cc_final: 0.8970 (tpt) REVERT: A 551 TRP cc_start: 0.9328 (t-100) cc_final: 0.8848 (t-100) REVERT: A 553 MET cc_start: 0.8927 (tpp) cc_final: 0.8718 (tpp) REVERT: B 54 LEU cc_start: 0.9398 (tp) cc_final: 0.9122 (tp) REVERT: B 81 VAL cc_start: 0.9632 (t) cc_final: 0.9430 (t) REVERT: B 109 LEU cc_start: 0.9623 (tp) cc_final: 0.9248 (tp) REVERT: B 110 MET cc_start: 0.8468 (mmt) cc_final: 0.8208 (mmm) REVERT: B 125 LEU cc_start: 0.9613 (tp) cc_final: 0.9276 (tp) REVERT: B 294 MET cc_start: 0.8604 (ppp) cc_final: 0.8058 (ppp) REVERT: B 322 ASP cc_start: 0.9376 (p0) cc_final: 0.8960 (p0) REVERT: B 442 MET cc_start: 0.9585 (ttt) cc_final: 0.9055 (tpt) REVERT: B 504 MET cc_start: 0.8920 (mmp) cc_final: 0.8468 (tpp) REVERT: B 553 MET cc_start: 0.8942 (tpp) cc_final: 0.8680 (tpp) REVERT: M 706 GLU cc_start: 0.9114 (tp30) cc_final: 0.8852 (tp30) REVERT: P 697 GLU cc_start: 0.9165 (tt0) cc_final: 0.8239 (pp20) REVERT: P 703 LYS cc_start: 0.9377 (tptm) cc_final: 0.9152 (tptm) REVERT: P 706 GLU cc_start: 0.9181 (tp30) cc_final: 0.8517 (tp30) REVERT: P 720 ARG cc_start: 0.5679 (mmp80) cc_final: 0.3576 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1075 time to fit residues: 21.1608 Evaluate side-chains 95 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.0040 chunk 46 optimal weight: 0.0770 chunk 73 optimal weight: 0.0470 chunk 74 optimal weight: 7.9990 overall best weight: 0.6252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS P 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036121 restraints weight = 62986.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037555 restraints weight = 41391.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038638 restraints weight = 30491.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.039439 restraints weight = 24157.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040003 restraints weight = 20217.358| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11080 Z= 0.110 Angle : 0.693 7.010 15066 Z= 0.345 Chirality : 0.047 0.195 1720 Planarity : 0.004 0.061 1876 Dihedral : 7.265 76.386 1398 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: -2.46 (0.23), residues: 1254 helix: -0.79 (0.36), residues: 178 sheet: -0.38 (0.39), residues: 158 loop : -2.22 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.024 0.001 TYR N 19 PHE 0.016 0.001 PHE P 714 TRP 0.008 0.001 TRP B 551 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11022) covalent geometry : angle 0.66628 / 0.34 (14922) SS BOND : bond 0.00255 / 0.19 ( 30) SS BOND : angle 1.62185 / 1.23 ( 60) hydrogen bonds : bond 0.04426 / 2.97 ( 226) hydrogen bonds : angle 7.28747 / 4.83 ( 588) link_BETA1-4 : bond 0.00464 / 0.33 ( 10) link_BETA1-4 : angle 1.97800 / 1.51 ( 30) link_BETA1-6 : bond 0.00462 / 0.26 ( 6) link_BETA1-6 : angle 1.27005 / 0.92 ( 18) link_NAG-ASN : bond 0.00431 / 0.33 ( 12) link_NAG-ASN : angle 2.93311 / 1.83 ( 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 123 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.525 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: 0.9334 (mt0) cc_final: 0.9042 (mt0) REVERT: A 81 VAL cc_start: 0.9606 (t) cc_final: 0.9287 (t) REVERT: A 98 MET cc_start: 0.8582 (tpp) cc_final: 0.8060 (mmt) REVERT: A 101 LEU cc_start: 0.9794 (tp) cc_final: 0.9530 (mt) REVERT: A 109 LEU cc_start: 0.9735 (tp) cc_final: 0.9530 (tp) REVERT: A 110 MET cc_start: 0.8508 (mmp) cc_final: 0.8093 (mmm) REVERT: A 120 GLU cc_start: 0.9247 (tt0) cc_final: 0.8694 (tt0) REVERT: A 125 LEU cc_start: 0.9731 (tp) cc_final: 0.9519 (tp) REVERT: A 150 ASP cc_start: 0.8934 (p0) cc_final: 0.8270 (m-30) REVERT: A 294 MET cc_start: 0.8379 (ppp) cc_final: 0.7834 (ppp) REVERT: A 322 ASP cc_start: 0.9260 (p0) cc_final: 0.8886 (p0) REVERT: A 442 MET cc_start: 0.9552 (ttt) cc_final: 0.9055 (tpt) REVERT: A 553 MET cc_start: 0.8815 (tpp) cc_final: 0.8554 (tpp) REVERT: B 34 GLN cc_start: 0.9546 (mt0) cc_final: 0.9344 (mt0) REVERT: B 38 MET cc_start: 0.8591 (mtt) cc_final: 0.8377 (mtt) REVERT: B 54 LEU cc_start: 0.9402 (tp) cc_final: 0.9136 (tp) REVERT: B 109 LEU cc_start: 0.9612 (tp) cc_final: 0.9406 (tp) REVERT: B 294 MET cc_start: 0.8469 (ppp) cc_final: 0.7919 (ppp) REVERT: B 322 ASP cc_start: 0.9326 (p0) cc_final: 0.8910 (p0) REVERT: B 442 MET cc_start: 0.9565 (ttt) cc_final: 0.9082 (tpt) REVERT: B 553 MET cc_start: 0.8824 (tpp) cc_final: 0.8490 (tpp) REVERT: M 703 LYS cc_start: 0.9376 (tptm) cc_final: 0.9042 (tptm) REVERT: M 706 GLU cc_start: 0.9213 (tp30) cc_final: 0.8721 (tp30) REVERT: O 13 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9310 (mm-30) REVERT: P 703 LYS cc_start: 0.9352 (tptm) cc_final: 0.9103 (tptm) REVERT: P 706 GLU cc_start: 0.9296 (tp30) cc_final: 0.8943 (tp30) REVERT: P 720 ARG cc_start: 0.5701 (mmp80) cc_final: 0.3506 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1057 time to fit residues: 18.9639 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 : 0.468 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 410 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 410 GLN L 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.035914 restraints weight = 62451.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037293 restraints weight = 41153.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.038362 restraints weight = 30613.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039072 restraints weight = 24267.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039697 restraints weight = 20571.802| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11080 Z= 0.110 Angle : 0.669 8.459 15066 Z= 0.331 Chirality : 0.046 0.188 1720 Planarity : 0.005 0.057 1876 Dihedral : 6.931 74.800 1398 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -2.27 (0.24), residues: 1254 helix: -0.83 (0.37), residues: 178 sheet: -0.59 (0.36), residues: 176 loop : -1.99 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 539 TYR 0.022 0.001 TYR N 19 PHE 0.016 0.001 PHE B 382 TRP 0.013 0.001 TRP A 551 HIS 0.006 0.001 HIS O 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11022) covalent geometry : angle 0.64662 / 0.33 (14922) SS BOND : bond 0.00328 / 0.20 ( 30) SS BOND : angle 1.28751 / 0.92 ( 60) hydrogen bonds : bond 0.04034 / 2.68 ( 226) hydrogen bonds : angle 6.81948 / 4.50 ( 588) link_BETA1-4 : bond 0.00372 / 0.28 ( 10) link_BETA1-4 : angle 1.93698 / 1.45 ( 30) link_BETA1-6 : bond 0.00417 / 0.23 ( 6) link_BETA1-6 : angle 1.23900 / 0.91 ( 18) link_NAG-ASN : bond 0.00408 / 0.32 ( 12) link_NAG-ASN : angle 2.70125 / 1.66 ( 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 116 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.439 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: 0.9340 (mt0) cc_final: 0.9028 (mt0) REVERT: A 81 VAL cc_start: 0.9605 (t) cc_final: 0.9257 (t) REVERT: A 98 MET cc_start: 0.8664 (tpp) cc_final: 0.8183 (mmt) REVERT: A 101 LEU cc_start: 0.9788 (tp) cc_final: 0.9502 (mt) REVERT: A 109 LEU cc_start: 0.9748 (tp) cc_final: 0.9532 (tp) REVERT: A 110 MET cc_start: 0.8517 (mmp) cc_final: 0.8081 (mmm) REVERT: A 125 LEU cc_start: 0.9736 (tp) cc_final: 0.9536 (tp) REVERT: A 150 ASP cc_start: 0.8941 (p0) cc_final: 0.8507 (m-30) REVERT: A 294 MET cc_start: 0.8378 (ppp) cc_final: 0.7921 (ppp) REVERT: A 322 ASP cc_start: 0.9282 (p0) cc_final: 0.8924 (p0) REVERT: A 442 MET cc_start: 0.9530 (ttt) cc_final: 0.9046 (tpt) REVERT: A 552 LEU cc_start: 0.9544 (tp) cc_final: 0.9324 (tp) REVERT: B 54 LEU cc_start: 0.9411 (tp) cc_final: 0.9158 (tp) REVERT: B 294 MET cc_start: 0.8493 (ppp) cc_final: 0.7962 (ppp) REVERT: B 322 ASP cc_start: 0.9320 (p0) cc_final: 0.8873 (p0) REVERT: B 442 MET cc_start: 0.9552 (ttt) cc_final: 0.9018 (tpt) REVERT: B 486 LEU cc_start: 0.9600 (tp) cc_final: 0.9376 (tp) REVERT: B 553 MET cc_start: 0.8823 (tpp) cc_final: 0.8470 (tpp) REVERT: M 703 LYS cc_start: 0.9396 (tptm) cc_final: 0.9056 (tptm) REVERT: M 706 GLU cc_start: 0.9170 (tp30) cc_final: 0.8622 (tp30) REVERT: O 13 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9257 (mm-30) REVERT: P 703 LYS cc_start: 0.9339 (tptm) cc_final: 0.9041 (tptt) REVERT: P 706 GLU cc_start: 0.9360 (tp30) cc_final: 0.8942 (tp30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1005 time to fit residues: 17.3129 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 : 0.701 ------------------------------------------------------------------------------- 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: 10.0000 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN 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 328 GLN B 410 GLN B 431 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033737 restraints weight = 66322.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.034975 restraints weight = 45257.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035893 restraints weight = 34115.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036579 restraints weight = 27606.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.037079 restraints weight = 23469.091| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3393 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= 0.246 Angle : 0.788 6.601 15066 Z= 0.381 Chirality : 0.047 0.178 1720 Planarity : 0.005 0.061 1876 Dihedral : 7.111 73.366 1398 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -2.27 (0.24), residues: 1254 helix: -1.08 (0.36), residues: 180 sheet: -0.44 (0.36), residues: 176 loop : -1.97 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 498 TYR 0.028 0.002 TYR N 19 PHE 0.056 0.002 PHE P 714 TRP 0.010 0.002 TRP A 183 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 (11022) covalent geometry : angle 0.76894 / 0.38 (14922) SS BOND : bond 0.00406 / 0.24 ( 30) SS BOND : angle 1.36312 / 1.03 ( 60) hydrogen bonds : bond 0.04206 / 2.81 ( 226) hydrogen bonds : angle 6.93349 / 4.56 ( 588) link_BETA1-4 : bond 0.00374 / 0.27 ( 10) link_BETA1-4 : angle 1.97412 / 1.46 ( 30) link_BETA1-6 : bond 0.00339 / 0.18 ( 6) link_BETA1-6 : angle 1.49268 / 1.11 ( 18) link_NAG-ASN : bond 0.00311 / 0.24 ( 12) link_NAG-ASN : angle 2.74646 / 1.67 ( 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 108 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.467 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: A 34 GLN cc_start: 0.9148 (mt0) cc_final: 0.8847 (mt0) REVERT: A 81 VAL cc_start: 0.9648 (t) cc_final: 0.9279 (t) REVERT: A 98 MET cc_start: 0.8555 (tpp) cc_final: 0.8233 (mmt) REVERT: A 101 LEU cc_start: 0.9805 (tp) cc_final: 0.9497 (mt) REVERT: A 109 LEU cc_start: 0.9761 (tp) cc_final: 0.9560 (tp) REVERT: A 110 MET cc_start: 0.8615 (mmp) cc_final: 0.8322 (mmm) REVERT: A 294 MET cc_start: 0.8287 (ppp) cc_final: 0.7781 (ppp) REVERT: A 322 ASP cc_start: 0.9304 (p0) cc_final: 0.8952 (p0) REVERT: A 442 MET cc_start: 0.9590 (ttt) cc_final: 0.9230 (tmm) REVERT: A 479 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7871 (ttp80) REVERT: A 486 LEU cc_start: 0.9690 (tp) cc_final: 0.9004 (tp) REVERT: A 504 MET cc_start: 0.9032 (mmm) cc_final: 0.8749 (mmm) REVERT: B 34 GLN cc_start: 0.9379 (mt0) cc_final: 0.9061 (mt0) REVERT: B 54 LEU cc_start: 0.9505 (tp) cc_final: 0.9282 (tp) REVERT: B 98 MET cc_start: 0.8688 (mmm) cc_final: 0.8325 (mmm) REVERT: B 101 LEU cc_start: 0.9709 (mt) cc_final: 0.9497 (mm) REVERT: B 294 MET cc_start: 0.8513 (ppp) cc_final: 0.8081 (ppp) REVERT: B 322 ASP cc_start: 0.9361 (p0) cc_final: 0.9007 (p0) REVERT: B 442 MET cc_start: 0.9611 (ttt) cc_final: 0.9104 (tpt) REVERT: B 479 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8002 (ttp80) REVERT: B 486 LEU cc_start: 0.9673 (tp) cc_final: 0.8894 (mt) REVERT: B 504 MET cc_start: 0.9301 (mmp) cc_final: 0.8946 (mmm) REVERT: B 553 MET cc_start: 0.8945 (tpp) cc_final: 0.8603 (tpp) REVERT: M 695 GLU cc_start: 0.9073 (mp0) cc_final: 0.8757 (mp0) REVERT: M 703 LYS cc_start: 0.9440 (tptm) cc_final: 0.9124 (tptm) REVERT: M 706 GLU cc_start: 0.9229 (tp30) cc_final: 0.8688 (tp30) REVERT: L 13 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9350 (mm-30) REVERT: O 13 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9274 (mm-30) REVERT: P 703 LYS cc_start: 0.9402 (tptm) cc_final: 0.9097 (tptt) REVERT: P 706 GLU cc_start: 0.9440 (tp30) cc_final: 0.8945 (tp30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1096 time to fit residues: 16.9681 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 : 0.434 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3109 r_free = 0.3109 target = 0.046689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.034992 restraints weight = 63440.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.036371 restraints weight = 41729.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.037405 restraints weight = 30692.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038166 restraints weight = 24330.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038702 restraints weight = 20349.787| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3566 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= 0.113 Angle : 0.663 8.283 15066 Z= 0.327 Chirality : 0.046 0.186 1720 Planarity : 0.004 0.057 1876 Dihedral : 6.722 71.804 1398 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -2.18 (0.24), residues: 1254 helix: -0.92 (0.37), residues: 180 sheet: -0.44 (0.35), residues: 176 loop : -1.90 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.027 0.001 TYR N 19 PHE 0.048 0.002 PHE M 714 TRP 0.008 0.001 TRP B 551 HIS 0.002 0.001 HIS O 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11022) covalent geometry : angle 0.64300 / 0.32 (14922) SS BOND : bond 0.00266 / 0.19 ( 30) SS BOND : angle 1.09032 / 0.84 ( 60) hydrogen bonds : bond 0.03804 / 2.53 ( 226) hydrogen bonds : angle 6.54871 / 4.31 ( 588) link_BETA1-4 : bond 0.00381 / 0.28 ( 10) link_BETA1-4 : angle 1.81038 / 1.35 ( 30) link_BETA1-6 : bond 0.00420 / 0.23 ( 6) link_BETA1-6 : angle 1.28585 / 0.94 ( 18) link_NAG-ASN : bond 0.00352 / 0.27 ( 12) link_NAG-ASN : angle 2.66791 / 1.64 ( 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 111 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.451 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: 0.9265 (mt0) cc_final: 0.8959 (mt0) REVERT: A 81 VAL cc_start: 0.9611 (t) cc_final: 0.9249 (t) REVERT: A 101 LEU cc_start: 0.9764 (tp) cc_final: 0.9511 (mt) REVERT: A 109 LEU cc_start: 0.9751 (tp) cc_final: 0.9437 (tp) REVERT: A 110 MET cc_start: 0.8523 (mmp) cc_final: 0.8048 (mmm) REVERT: A 322 ASP cc_start: 0.9159 (p0) cc_final: 0.8796 (p0) REVERT: A 442 MET cc_start: 0.9542 (ttt) cc_final: 0.9091 (tmm) REVERT: A 504 MET cc_start: 0.9019 (mmm) cc_final: 0.8736 (mmm) REVERT: B 34 GLN cc_start: 0.9365 (mt0) cc_final: 0.9042 (mt0) REVERT: B 54 LEU cc_start: 0.9476 (tp) cc_final: 0.9217 (tp) REVERT: B 98 MET cc_start: 0.8579 (mmm) cc_final: 0.8237 (mmm) REVERT: B 101 LEU cc_start: 0.9666 (mt) cc_final: 0.9418 (mm) REVERT: B 109 LEU cc_start: 0.9637 (tp) cc_final: 0.9434 (tp) REVERT: B 322 ASP cc_start: 0.9197 (p0) cc_final: 0.8775 (p0) REVERT: B 442 MET cc_start: 0.9541 (ttt) cc_final: 0.9023 (tpt) REVERT: B 486 LEU cc_start: 0.9623 (tp) cc_final: 0.9417 (tp) REVERT: B 504 MET cc_start: 0.9286 (mmp) cc_final: 0.9039 (mmm) REVERT: B 553 MET cc_start: 0.8875 (tpp) cc_final: 0.8478 (tpp) REVERT: M 695 GLU cc_start: 0.9133 (mp0) cc_final: 0.8836 (mp0) REVERT: M 703 LYS cc_start: 0.9412 (tptm) cc_final: 0.9066 (tptm) REVERT: M 706 GLU cc_start: 0.9168 (tp30) cc_final: 0.8535 (tp30) REVERT: L 13 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9315 (mm-30) REVERT: O 13 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9259 (mm-30) REVERT: P 696 LEU cc_start: 0.9381 (mt) cc_final: 0.8896 (tt) REVERT: P 703 LYS cc_start: 0.9369 (tptm) cc_final: 0.9079 (tptm) REVERT: P 706 GLU cc_start: 0.9438 (tp30) cc_final: 0.8918 (tp30) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1002 time to fit residues: 16.6988 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 : 0.515 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.0000 chunk 49 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 209 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 = 0.3122 r_free = 0.3122 target = 0.046782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034864 restraints weight = 62985.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.036193 restraints weight = 42151.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.037108 restraints weight = 31586.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037923 restraints weight = 25633.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038518 restraints weight = 21419.876| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11080 Z= 0.110 Angle : 0.660 9.863 15066 Z= 0.320 Chirality : 0.046 0.190 1720 Planarity : 0.004 0.053 1876 Dihedral : 6.571 69.546 1398 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -2.09 (0.24), residues: 1254 helix: -0.86 (0.38), residues: 180 sheet: -0.29 (0.36), residues: 176 loop : -1.86 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.024 0.001 TYR N 19 PHE 0.038 0.002 PHE M 714 TRP 0.007 0.001 TRP B 551 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11022) covalent geometry : angle 0.64058 / 0.32 (14922) SS BOND : bond 0.00330 / 0.24 ( 30) SS BOND : angle 1.08959 / 0.79 ( 60) hydrogen bonds : bond 0.03614 / 2.42 ( 226) hydrogen bonds : angle 6.34470 / 4.20 ( 588) link_BETA1-4 : bond 0.00371 / 0.28 ( 10) link_BETA1-4 : angle 1.82456 / 1.36 ( 30) link_BETA1-6 : bond 0.00389 / 0.22 ( 6) link_BETA1-6 : angle 1.28368 / 0.93 ( 18) link_NAG-ASN : bond 0.00320 / 0.23 ( 12) link_NAG-ASN : angle 2.52690 / 1.53 ( 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 106 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.444 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: A 34 GLN cc_start: 0.9205 (mt0) cc_final: 0.8880 (mt0) REVERT: A 81 VAL cc_start: 0.9609 (t) cc_final: 0.9188 (t) REVERT: A 98 MET cc_start: 0.9138 (mmm) cc_final: 0.8629 (mmm) REVERT: A 109 LEU cc_start: 0.9753 (tp) cc_final: 0.9533 (tp) REVERT: A 110 MET cc_start: 0.8457 (mmp) cc_final: 0.8161 (mmm) REVERT: A 322 ASP cc_start: 0.9168 (p0) cc_final: 0.8779 (p0) REVERT: A 442 MET cc_start: 0.9531 (ttt) cc_final: 0.9079 (tmm) REVERT: A 473 LEU cc_start: 0.9206 (mt) cc_final: 0.9002 (mt) REVERT: A 504 MET cc_start: 0.8983 (mmm) cc_final: 0.8718 (mmm) REVERT: B 34 GLN cc_start: 0.9307 (mt0) cc_final: 0.9025 (mt0) REVERT: B 54 LEU cc_start: 0.9463 (tp) cc_final: 0.9257 (tp) REVERT: B 98 MET cc_start: 0.8654 (mmm) cc_final: 0.7965 (mmm) REVERT: B 442 MET cc_start: 0.9548 (ttt) cc_final: 0.9066 (tpt) REVERT: B 486 LEU cc_start: 0.9617 (tp) cc_final: 0.9405 (tp) REVERT: B 504 MET cc_start: 0.9261 (mmp) cc_final: 0.9034 (mmm) REVERT: B 553 MET cc_start: 0.8881 (tpp) cc_final: 0.8481 (tpp) REVERT: M 695 GLU cc_start: 0.9074 (mp0) cc_final: 0.8867 (mp0) REVERT: M 703 LYS cc_start: 0.9407 (tptm) cc_final: 0.9060 (tptm) REVERT: M 706 GLU cc_start: 0.9196 (tp30) cc_final: 0.8560 (tp30) REVERT: L 13 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9312 (mm-30) REVERT: O 13 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9267 (mm-30) REVERT: P 695 GLU cc_start: 0.9099 (mp0) cc_final: 0.8803 (mp0) REVERT: P 696 LEU cc_start: 0.9396 (mt) cc_final: 0.8975 (tt) REVERT: P 703 LYS cc_start: 0.9381 (tptm) cc_final: 0.9106 (tptm) REVERT: P 706 GLU cc_start: 0.9432 (tp30) cc_final: 0.8911 (tp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1017 time to fit residues: 16.0339 Evaluate side-chains 85 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 0.0570 chunk 82 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 0.0670 overall best weight: 0.6356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3131 r_free = 0.3131 target = 0.047048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.035170 restraints weight = 63503.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036539 restraints weight = 42013.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037558 restraints weight = 31095.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038180 restraints weight = 24808.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038830 restraints weight = 21171.949| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11080 Z= 0.099 Angle : 0.647 8.431 15066 Z= 0.315 Chirality : 0.045 0.193 1720 Planarity : 0.004 0.054 1876 Dihedral : 6.304 66.685 1398 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.03 (0.24), residues: 1254 helix: -0.77 (0.39), residues: 178 sheet: -0.22 (0.36), residues: 176 loop : -1.83 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 14 TYR 0.021 0.001 TYR N 19 PHE 0.029 0.001 PHE M 714 TRP 0.007 0.001 TRP A 493 HIS 0.003 0.000 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (11022) covalent geometry : angle 0.62884 / 0.31 (14922) SS BOND : bond 0.00264 / 0.19 ( 30) SS BOND : angle 0.99640 / 0.74 ( 60) hydrogen bonds : bond 0.03556 / 2.37 ( 226) hydrogen bonds : angle 6.16399 / 4.07 ( 588) link_BETA1-4 : bond 0.00400 / 0.29 ( 10) link_BETA1-4 : angle 1.77324 / 1.32 ( 30) link_BETA1-6 : bond 0.00432 / 0.24 ( 6) link_BETA1-6 : angle 1.21946 / 0.88 ( 18) link_NAG-ASN : bond 0.00343 / 0.25 ( 12) link_NAG-ASN : angle 2.48224 / 1.50 ( 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 109 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.397 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: 0.9198 (mt0) cc_final: 0.8900 (mt0) REVERT: A 81 VAL cc_start: 0.9595 (t) cc_final: 0.9175 (t) REVERT: A 98 MET cc_start: 0.9097 (mmm) cc_final: 0.8292 (mmm) REVERT: A 101 LEU cc_start: 0.9659 (mt) cc_final: 0.9351 (mm) REVERT: A 109 LEU cc_start: 0.9756 (tp) cc_final: 0.9415 (tp) REVERT: A 110 MET cc_start: 0.8472 (mmp) cc_final: 0.8061 (mmm) REVERT: A 322 ASP cc_start: 0.9143 (p0) cc_final: 0.8735 (p0) REVERT: A 357 ASN cc_start: 0.8735 (p0) cc_final: 0.8427 (t0) REVERT: A 442 MET cc_start: 0.9526 (ttt) cc_final: 0.9061 (tmm) REVERT: A 473 LEU cc_start: 0.9220 (mt) cc_final: 0.9019 (mt) REVERT: A 504 MET cc_start: 0.8996 (mmm) cc_final: 0.8723 (mmm) REVERT: A 552 LEU cc_start: 0.9583 (tp) cc_final: 0.9292 (tp) REVERT: B 34 GLN cc_start: 0.9320 (mt0) cc_final: 0.8984 (mt0) REVERT: B 38 MET cc_start: 0.9004 (mmt) cc_final: 0.8350 (mmm) REVERT: B 98 MET cc_start: 0.8606 (mmm) cc_final: 0.8002 (mmm) REVERT: B 442 MET cc_start: 0.9545 (ttt) cc_final: 0.9053 (tpt) REVERT: B 486 LEU cc_start: 0.9616 (tp) cc_final: 0.9403 (tp) REVERT: B 504 MET cc_start: 0.9283 (mmp) cc_final: 0.9056 (mmm) REVERT: B 553 MET cc_start: 0.8928 (tpp) cc_final: 0.8520 (tpp) REVERT: M 695 GLU cc_start: 0.9109 (mp0) cc_final: 0.8891 (mp0) REVERT: M 703 LYS cc_start: 0.9412 (tptm) cc_final: 0.9065 (tptm) REVERT: M 706 GLU cc_start: 0.9167 (tp30) cc_final: 0.8529 (tp30) REVERT: L 9 SER cc_start: 0.9327 (m) cc_final: 0.8855 (m) REVERT: L 13 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9324 (mm-30) REVERT: O 13 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9289 (mm-30) REVERT: P 695 GLU cc_start: 0.9140 (mp0) cc_final: 0.8859 (mp0) REVERT: P 696 LEU cc_start: 0.9420 (mt) cc_final: 0.8994 (tt) REVERT: P 703 LYS cc_start: 0.9366 (tptm) cc_final: 0.9103 (tptm) REVERT: P 706 GLU cc_start: 0.9446 (tp30) cc_final: 0.8862 (tp30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0866 time to fit residues: 14.0972 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 : 0.337 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3117 r_free = 0.3117 target = 0.046494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034710 restraints weight = 64574.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036004 restraints weight = 43283.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037000 restraints weight = 32441.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037721 restraints weight = 25982.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038271 restraints weight = 21932.532| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11080 Z= 0.134 Angle : 0.660 7.670 15066 Z= 0.320 Chirality : 0.045 0.189 1720 Planarity : 0.004 0.051 1876 Dihedral : 6.245 63.742 1398 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -1.95 (0.24), residues: 1254 helix: -0.79 (0.38), residues: 178 sheet: -0.02 (0.37), residues: 172 loop : -1.79 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 22 TYR 0.020 0.001 TYR N 19 PHE 0.032 0.002 PHE M 714 TRP 0.010 0.001 TRP B 559 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11022) covalent geometry : angle 0.64245 / 0.32 (14922) SS BOND : bond 0.00258 / 0.19 ( 30) SS BOND : angle 0.97121 / 0.71 ( 60) hydrogen bonds : bond 0.03534 / 2.37 ( 226) hydrogen bonds : angle 6.16265 / 4.07 ( 588) link_BETA1-4 : bond 0.00353 / 0.26 ( 10) link_BETA1-4 : angle 1.75948 / 1.32 ( 30) link_BETA1-6 : bond 0.00315 / 0.17 ( 6) link_BETA1-6 : angle 1.29912 / 0.95 ( 18) link_NAG-ASN : bond 0.00297 / 0.23 ( 12) link_NAG-ASN : angle 2.45968 / 1.48 ( 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 103 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9139 (mt0) cc_final: 0.8734 (mt0) REVERT: A 81 VAL cc_start: 0.9606 (t) cc_final: 0.9163 (t) REVERT: A 98 MET cc_start: 0.9041 (mmm) cc_final: 0.8290 (mmm) REVERT: A 101 LEU cc_start: 0.9658 (mt) cc_final: 0.9342 (mm) REVERT: A 109 LEU cc_start: 0.9757 (tp) cc_final: 0.9404 (tp) REVERT: A 110 MET cc_start: 0.8448 (mmp) cc_final: 0.8055 (mmm) REVERT: A 322 ASP cc_start: 0.9141 (p0) cc_final: 0.8739 (p0) REVERT: A 357 ASN cc_start: 0.8783 (p0) cc_final: 0.8495 (t0) REVERT: A 442 MET cc_start: 0.9530 (ttt) cc_final: 0.9135 (tmm) REVERT: A 479 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7818 (ttp80) REVERT: A 486 LEU cc_start: 0.9647 (tp) cc_final: 0.8896 (tp) REVERT: A 504 MET cc_start: 0.8994 (mmm) cc_final: 0.8720 (mmm) REVERT: B 34 GLN cc_start: 0.9321 (mt0) cc_final: 0.8927 (mt0) REVERT: B 81 VAL cc_start: 0.9598 (t) cc_final: 0.9392 (t) REVERT: B 98 MET cc_start: 0.8703 (mmm) cc_final: 0.8068 (mmm) REVERT: B 442 MET cc_start: 0.9560 (ttt) cc_final: 0.9082 (tpt) REVERT: B 486 LEU cc_start: 0.9646 (tp) cc_final: 0.8933 (mt) REVERT: B 504 MET cc_start: 0.9262 (mmp) cc_final: 0.8924 (mmm) REVERT: B 552 LEU cc_start: 0.9551 (tp) cc_final: 0.9277 (tp) REVERT: B 553 MET cc_start: 0.8897 (tpp) cc_final: 0.8648 (tpp) REVERT: M 695 GLU cc_start: 0.9120 (mp0) cc_final: 0.8911 (mp0) REVERT: M 703 LYS cc_start: 0.9396 (tptm) cc_final: 0.9059 (tptm) REVERT: M 706 GLU cc_start: 0.9326 (tp30) cc_final: 0.8862 (tp30) REVERT: L 13 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9347 (mm-30) REVERT: O 13 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9311 (mm-30) REVERT: P 695 GLU cc_start: 0.9139 (mp0) cc_final: 0.8933 (mp0) REVERT: P 703 LYS cc_start: 0.9390 (tptm) cc_final: 0.9122 (tptm) REVERT: P 706 GLU cc_start: 0.9379 (tp30) cc_final: 0.8816 (tp30) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0895 time to fit residues: 14.0827 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 : 0.420 ------------------------------------------------------------------------------- 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: 8.9990 chunk 121 optimal weight: 0.0670 chunk 83 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3154 r_free = 0.3154 target = 0.047830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035788 restraints weight = 62853.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037179 restraints weight = 41722.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038200 restraints weight = 30940.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038948 restraints weight = 24723.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039541 restraints weight = 20932.826| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11080 Z= 0.098 Angle : 0.655 8.094 15066 Z= 0.315 Chirality : 0.046 0.236 1720 Planarity : 0.004 0.055 1876 Dihedral : 6.055 60.074 1398 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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 : 0.17 % 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: -1.93 (0.24), residues: 1254 helix: -0.65 (0.39), residues: 178 sheet: 0.04 (0.37), residues: 172 loop : -1.82 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.018 0.001 TYR N 19 PHE 0.024 0.001 PHE M 714 TRP 0.010 0.001 TRP B 551 HIS 0.004 0.000 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11022) covalent geometry : angle 0.63847 / 0.31 (14922) SS BOND : bond 0.00304 / 0.19 ( 30) SS BOND : angle 0.98973 / 0.70 ( 60) hydrogen bonds : bond 0.03436 / 2.27 ( 226) hydrogen bonds : angle 5.97915 / 3.95 ( 588) link_BETA1-4 : bond 0.00414 / 0.31 ( 10) link_BETA1-4 : angle 1.69082 / 1.25 ( 30) link_BETA1-6 : bond 0.00588 / 0.37 ( 6) link_BETA1-6 : angle 1.35677 / 0.99 ( 18) link_NAG-ASN : bond 0.00328 / 0.25 ( 12) link_NAG-ASN : angle 2.37707 / 1.41 ( 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 113 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9217 (mt0) cc_final: 0.8919 (mt0) REVERT: A 81 VAL cc_start: 0.9614 (t) cc_final: 0.9142 (t) REVERT: A 98 MET cc_start: 0.9047 (mmm) cc_final: 0.8379 (mmm) REVERT: A 101 LEU cc_start: 0.9641 (mt) cc_final: 0.9326 (mm) REVERT: A 109 LEU cc_start: 0.9772 (tp) cc_final: 0.9530 (tp) REVERT: A 110 MET cc_start: 0.8324 (mmp) cc_final: 0.8076 (mmm) REVERT: A 322 ASP cc_start: 0.9127 (p0) cc_final: 0.8746 (p0) REVERT: A 357 ASN cc_start: 0.8680 (p0) cc_final: 0.8359 (t0) REVERT: A 442 MET cc_start: 0.9526 (ttt) cc_final: 0.9067 (tmm) REVERT: A 486 LEU cc_start: 0.9657 (tp) cc_final: 0.8947 (tp) REVERT: A 504 MET cc_start: 0.9010 (mmm) cc_final: 0.8749 (mmm) REVERT: A 552 LEU cc_start: 0.9611 (tp) cc_final: 0.9249 (tp) REVERT: B 38 MET cc_start: 0.8732 (mmm) cc_final: 0.7878 (mmm) REVERT: B 98 MET cc_start: 0.8622 (mmm) cc_final: 0.7995 (mmm) REVERT: B 442 MET cc_start: 0.9526 (ttt) cc_final: 0.9062 (tpt) REVERT: B 504 MET cc_start: 0.9281 (mmp) cc_final: 0.9060 (mmm) REVERT: B 553 MET cc_start: 0.8729 (tpp) cc_final: 0.8327 (tpp) REVERT: M 695 GLU cc_start: 0.9127 (mp0) cc_final: 0.8903 (mp0) REVERT: M 706 GLU cc_start: 0.9330 (tp30) cc_final: 0.8851 (tp30) REVERT: L 9 SER cc_start: 0.9282 (m) cc_final: 0.8913 (m) REVERT: L 13 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9350 (mm-30) REVERT: O 13 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9326 (mm-30) REVERT: P 695 GLU cc_start: 0.9136 (mp0) cc_final: 0.8926 (mp0) REVERT: P 703 LYS cc_start: 0.9356 (tptm) cc_final: 0.9084 (tptm) REVERT: P 706 GLU cc_start: 0.9410 (tp30) cc_final: 0.8802 (tp30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0851 time to fit residues: 14.8087 Evaluate side-chains 90 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 0.8980 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 100 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 126 optimal weight: 3.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3158 r_free = 0.3158 target = 0.047805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035786 restraints weight = 62852.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037157 restraints weight = 41667.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038099 restraints weight = 30924.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038881 restraints weight = 25010.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039444 restraints weight = 21035.485| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11080 Z= 0.106 Angle : 0.677 15.192 15066 Z= 0.328 Chirality : 0.046 0.222 1720 Planarity : 0.004 0.054 1876 Dihedral : 5.941 56.883 1398 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.96 (0.24), residues: 1254 helix: -0.83 (0.38), residues: 178 sheet: 0.12 (0.37), residues: 170 loop : -1.82 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 479 TYR 0.035 0.001 TYR K 14 PHE 0.024 0.001 PHE M 714 TRP 0.008 0.001 TRP A 551 HIS 0.003 0.000 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11022) covalent geometry : angle 0.66287 / 0.32 (14922) SS BOND : bond 0.00250 / 0.17 ( 30) SS BOND : angle 0.98570 / 0.71 ( 60) hydrogen bonds : bond 0.03480 / 2.31 ( 226) hydrogen bonds : angle 6.00117 / 3.95 ( 588) link_BETA1-4 : bond 0.00386 / 0.28 ( 10) link_BETA1-4 : angle 1.66652 / 1.25 ( 30) link_BETA1-6 : bond 0.00595 / 0.38 ( 6) link_BETA1-6 : angle 1.29468 / 0.97 ( 18) link_NAG-ASN : bond 0.00304 / 0.23 ( 12) link_NAG-ASN : angle 2.17749 / 1.31 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.48 seconds wall clock time: 28 minutes 36.41 seconds (1716.41 seconds total)