Starting phenix.real_space_refine on Tue Jul 29 06:14:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.map" model { file = "/net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ce9_7462/07_2025/6ce9_7462.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10782 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "B" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "M" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "L" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "N" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "P" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.60, per 1000 atoms: 0.70 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: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.32 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: 3.40 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3437 1.34 - 1.47: 2720 1.47 - 1.59: 4755 1.59 - 1.71: 0 1.71 - 1.83: 110 Bond restraints: 11022 Sorted by residual: bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG B1015 " pdb=" O5 NAG B1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C1 NAG A1015 " pdb=" O5 NAG A1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 11017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14090 2.04 - 4.08: 679 4.08 - 6.13: 115 6.13 - 8.17: 34 8.17 - 10.21: 4 Bond angle restraints: 14922 Sorted by residual: angle pdb=" C HIS A 1 " pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C HIS B 1 " pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" N ASP A 542 " pdb=" CA ASP A 542 " pdb=" C ASP A 542 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" N ASP B 542 " pdb=" CA ASP B 542 " pdb=" C ASP B 542 " ideal model delta sigma weight residual 109.81 118.46 -8.65 2.21e+00 2.05e-01 1.53e+01 angle pdb=" N ILE A 136 " pdb=" CA ILE A 136 " pdb=" C ILE A 136 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 ... (remaining 14917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6778 21.38 - 42.75: 219 42.75 - 64.13: 21 64.13 - 85.51: 22 85.51 - 106.88: 8 Dihedral angle restraints: 7048 sinusoidal: 3298 harmonic: 3750 Sorted by residual: dihedral pdb=" CA CYS A 468 " pdb=" C CYS A 468 " pdb=" N GLU A 469 " pdb=" CA GLU A 469 " ideal model delta harmonic sigma weight residual -180.00 -129.36 -50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA CYS B 468 " pdb=" C CYS B 468 " pdb=" N GLU B 469 " pdb=" CA GLU B 469 " ideal model delta harmonic sigma weight residual -180.00 -129.40 -50.60 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL M 715 " pdb=" C VAL M 715 " pdb=" N PRO M 716 " pdb=" CA PRO M 716 " ideal model delta harmonic sigma weight residual 180.00 139.05 40.95 0 5.00e+00 4.00e-02 6.71e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1499 0.088 - 0.175: 208 0.175 - 0.263: 5 0.263 - 0.351: 4 0.351 - 0.439: 4 Chirality restraints: 1720 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 397 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 418 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 418 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 1717 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 715 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO P 716 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 716 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO P 716 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 715 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO M 716 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO M 716 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO M 716 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 715 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C VAL P 715 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL P 715 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO P 716 " -0.017 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3339 2.83 - 3.35: 9921 3.35 - 3.87: 18724 3.87 - 4.38: 20091 4.38 - 4.90: 33375 Nonbonded interactions: 85450 Sorted by model distance: nonbonded pdb=" O SER B 323 " pdb=" OG SER B 326 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 323 " pdb=" OG SER A 326 " model vdw 2.314 3.040 nonbonded pdb=" O CYS K 7 " pdb=" ND1 HIS L 5 " model vdw 2.314 3.120 nonbonded pdb=" O PRO A 558 " pdb=" OG1 THR A 560 " model vdw 2.314 3.040 nonbonded pdb=" O PRO B 558 " pdb=" OG1 THR B 560 " model vdw 2.314 3.040 ... (remaining 85445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.100 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 11080 Z= 0.379 Angle : 1.096 11.131 15066 Z= 0.558 Chirality : 0.061 0.439 1720 Planarity : 0.007 0.111 1876 Dihedral : 11.758 106.882 4534 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.60 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.003 TRP A 251 HIS 0.015 0.003 HIS A 199 PHE 0.046 0.004 PHE M 714 TYR 0.028 0.004 TYR N 19 ARG 0.007 0.001 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 12) link_NAG-ASN : angle 4.71706 ( 36) link_BETA1-4 : bond 0.00654 ( 10) link_BETA1-4 : angle 3.44492 ( 30) hydrogen bonds : bond 0.23962 ( 226) hydrogen bonds : angle 10.82059 ( 588) link_BETA1-6 : bond 0.00473 ( 6) link_BETA1-6 : angle 2.44403 ( 18) SS BOND : bond 0.00459 ( 30) SS BOND : angle 1.40484 ( 60) covalent geometry : bond 0.00783 (11022) covalent geometry : angle 1.05867 (14922) *********************** 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 : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9351 (mt0) cc_final: 0.9116 (mt0) REVERT: A 109 LEU cc_start: 0.9720 (tp) cc_final: 0.9497 (tp) REVERT: A 120 GLU cc_start: 0.9301 (tt0) cc_final: 0.9051 (tp30) REVERT: A 294 MET cc_start: 0.8546 (ppp) cc_final: 0.8067 (ppp) REVERT: A 322 ASP cc_start: 0.9403 (p0) cc_final: 0.9087 (p0) REVERT: A 442 MET cc_start: 0.9688 (ttt) cc_final: 0.9083 (tpt) REVERT: A 479 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8029 (ttp80) REVERT: A 480 THR cc_start: 0.8542 (p) cc_final: 0.8252 (t) REVERT: A 485 ILE cc_start: 0.9686 (mt) cc_final: 0.9464 (mm) REVERT: A 486 LEU cc_start: 0.9637 (tp) cc_final: 0.8914 (mt) REVERT: A 487 LEU cc_start: 0.9776 (mt) cc_final: 0.9453 (mm) REVERT: A 551 TRP cc_start: 0.9413 (t-100) cc_final: 0.8728 (t-100) REVERT: B 109 LEU cc_start: 0.9701 (tp) cc_final: 0.9386 (tp) REVERT: B 110 MET cc_start: 0.8619 (mmt) cc_final: 0.8336 (mmm) REVERT: B 178 PHE cc_start: 0.8918 (m-10) cc_final: 0.8592 (p90) REVERT: B 294 MET cc_start: 0.8709 (ppp) cc_final: 0.8201 (ppp) REVERT: B 322 ASP cc_start: 0.9462 (p0) cc_final: 0.9047 (p0) REVERT: B 376 LEU cc_start: 0.9377 (mt) cc_final: 0.9173 (tp) REVERT: B 442 MET cc_start: 0.9712 (ttt) cc_final: 0.9087 (tpt) REVERT: B 479 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8164 (ttp80) REVERT: B 486 LEU cc_start: 0.9658 (tp) cc_final: 0.9076 (mt) REVERT: B 487 LEU cc_start: 0.9722 (mt) cc_final: 0.9341 (mm) REVERT: L 11 LEU cc_start: 0.9625 (tp) cc_final: 0.9327 (tp) REVERT: L 18 VAL cc_start: 0.9290 (t) cc_final: 0.9038 (p) REVERT: P 697 GLU cc_start: 0.9193 (tt0) cc_final: 0.8752 (pt0) REVERT: P 707 ASP cc_start: 0.9202 (t70) cc_final: 0.8512 (t70) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2640 time to fit residues: 66.4883 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 : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 100 HIS A 187 HIS ** A 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 410 GLN K 18 ASN L 10 HIS O 10 HIS ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036058 restraints weight = 63915.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037445 restraints weight = 42137.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038470 restraints weight = 31143.897| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11080 Z= 0.152 Angle : 0.763 6.804 15066 Z= 0.380 Chirality : 0.049 0.237 1720 Planarity : 0.005 0.069 1876 Dihedral : 10.141 77.665 2000 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.23), residues: 1254 helix: -1.27 (0.34), residues: 182 sheet: -0.32 (0.39), residues: 154 loop : -2.41 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 551 HIS 0.004 0.001 HIS A 1 PHE 0.021 0.002 PHE P 714 TYR 0.028 0.002 TYR K 19 ARG 0.005 0.001 ARG B 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 12) link_NAG-ASN : angle 3.20102 ( 36) link_BETA1-4 : bond 0.00386 ( 10) link_BETA1-4 : angle 2.51492 ( 30) hydrogen bonds : bond 0.05509 ( 226) hydrogen bonds : angle 8.02327 ( 588) link_BETA1-6 : bond 0.00370 ( 6) link_BETA1-6 : angle 1.54862 ( 18) SS BOND : bond 0.00307 ( 30) SS BOND : angle 1.27742 ( 60) covalent geometry : bond 0.00316 (11022) covalent geometry : angle 0.73521 (14922) *********************** 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 139 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9381 (mt0) cc_final: 0.9096 (mt0) REVERT: A 81 VAL cc_start: 0.9670 (t) cc_final: 0.9267 (t) REVERT: A 98 MET cc_start: 0.8609 (tpp) cc_final: 0.8231 (mmm) REVERT: A 101 LEU cc_start: 0.9803 (tp) cc_final: 0.9583 (mt) REVERT: A 109 LEU cc_start: 0.9737 (tp) cc_final: 0.9515 (tp) REVERT: A 110 MET cc_start: 0.8542 (mmp) cc_final: 0.8104 (mmm) REVERT: A 120 GLU cc_start: 0.9314 (tt0) cc_final: 0.8949 (tt0) REVERT: A 125 LEU cc_start: 0.9732 (tp) cc_final: 0.9490 (tp) REVERT: A 150 ASP cc_start: 0.9090 (p0) cc_final: 0.8551 (m-30) REVERT: A 294 MET cc_start: 0.8576 (ppp) cc_final: 0.8066 (ppp) REVERT: A 322 ASP cc_start: 0.9329 (p0) cc_final: 0.8986 (p0) REVERT: A 442 MET cc_start: 0.9575 (ttt) cc_final: 0.8964 (tpt) REVERT: B 34 GLN cc_start: 0.9553 (mt0) cc_final: 0.9333 (mt0) REVERT: B 54 LEU cc_start: 0.9384 (tp) cc_final: 0.9105 (tp) REVERT: B 109 LEU cc_start: 0.9627 (tp) cc_final: 0.9267 (tp) REVERT: B 110 MET cc_start: 0.8501 (mmt) cc_final: 0.8241 (mmm) REVERT: B 294 MET cc_start: 0.8552 (ppp) cc_final: 0.8021 (ppp) REVERT: B 322 ASP cc_start: 0.9371 (p0) cc_final: 0.8972 (p0) REVERT: B 442 MET cc_start: 0.9591 (ttt) cc_final: 0.9125 (tpt) REVERT: B 504 MET cc_start: 0.8941 (mmp) cc_final: 0.8498 (tpp) REVERT: M 706 GLU cc_start: 0.9133 (tp30) cc_final: 0.8868 (tp30) REVERT: P 697 GLU cc_start: 0.9172 (tt0) cc_final: 0.8233 (pp20) REVERT: P 703 LYS cc_start: 0.9373 (tptm) cc_final: 0.9144 (tptm) REVERT: P 706 GLU cc_start: 0.9167 (tp30) cc_final: 0.8525 (tp30) REVERT: P 720 ARG cc_start: 0.5739 (mmp80) cc_final: 0.3470 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2390 time to fit residues: 47.1569 Evaluate side-chains 93 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS P 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.046427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.034723 restraints weight = 66051.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.036066 restraints weight = 43931.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037014 restraints weight = 32626.291| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11080 Z= 0.173 Angle : 0.740 7.040 15066 Z= 0.363 Chirality : 0.047 0.230 1720 Planarity : 0.005 0.063 1876 Dihedral : 8.698 76.499 2000 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.24), residues: 1254 helix: -0.98 (0.36), residues: 178 sheet: -0.53 (0.37), residues: 176 loop : -2.12 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 551 HIS 0.003 0.001 HIS L 5 PHE 0.021 0.002 PHE P 714 TYR 0.025 0.002 TYR K 19 ARG 0.004 0.000 ARG B 576 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 12) link_NAG-ASN : angle 3.04302 ( 36) link_BETA1-4 : bond 0.00460 ( 10) link_BETA1-4 : angle 2.47043 ( 30) hydrogen bonds : bond 0.04439 ( 226) hydrogen bonds : angle 7.29749 ( 588) link_BETA1-6 : bond 0.00371 ( 6) link_BETA1-6 : angle 1.48507 ( 18) SS BOND : bond 0.00308 ( 30) SS BOND : angle 1.69213 ( 60) covalent geometry : bond 0.00362 (11022) covalent geometry : angle 0.71033 (14922) *********************** 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 117 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.286 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: 0.9309 (mt0) cc_final: 0.9004 (mt0) REVERT: A 81 VAL cc_start: 0.9638 (t) cc_final: 0.9332 (t) REVERT: A 98 MET cc_start: 0.8561 (tpp) cc_final: 0.7966 (mmt) REVERT: A 101 LEU cc_start: 0.9812 (tp) cc_final: 0.9545 (mt) REVERT: A 110 MET cc_start: 0.8612 (mmp) cc_final: 0.8191 (mmm) REVERT: A 294 MET cc_start: 0.8387 (ppp) cc_final: 0.7785 (ppp) REVERT: A 322 ASP cc_start: 0.9263 (p0) cc_final: 0.8920 (p0) REVERT: A 442 MET cc_start: 0.9596 (ttt) cc_final: 0.9110 (tmm) REVERT: A 479 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7910 (ttp80) REVERT: A 486 LEU cc_start: 0.9673 (tp) cc_final: 0.8981 (mt) REVERT: A 551 TRP cc_start: 0.9323 (t-100) cc_final: 0.8865 (t-100) REVERT: B 34 GLN cc_start: 0.9470 (mt0) cc_final: 0.9135 (mt0) REVERT: B 54 LEU cc_start: 0.9447 (tp) cc_final: 0.9186 (tp) REVERT: B 294 MET cc_start: 0.8602 (ppp) cc_final: 0.8070 (ppp) REVERT: B 322 ASP cc_start: 0.9351 (p0) cc_final: 0.9068 (p0) REVERT: B 442 MET cc_start: 0.9617 (ttt) cc_final: 0.9105 (tpt) REVERT: B 553 MET cc_start: 0.8924 (tpp) cc_final: 0.8540 (tpp) REVERT: M 703 LYS cc_start: 0.9417 (tptm) cc_final: 0.9075 (tptm) REVERT: M 706 GLU cc_start: 0.9253 (tp30) cc_final: 0.8790 (tp30) REVERT: O 13 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9274 (mm-30) REVERT: P 697 GLU cc_start: 0.9159 (tt0) cc_final: 0.8278 (pp20) REVERT: P 703 LYS cc_start: 0.9393 (tptm) cc_final: 0.9146 (tptm) REVERT: P 706 GLU cc_start: 0.9364 (tp30) cc_final: 0.9009 (tp30) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.2243 time to fit residues: 37.8548 Evaluate side-chains 83 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034424 restraints weight = 65397.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035703 restraints weight = 43717.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.036681 restraints weight = 32619.702| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11080 Z= 0.181 Angle : 0.735 10.600 15066 Z= 0.358 Chirality : 0.047 0.231 1720 Planarity : 0.005 0.060 1876 Dihedral : 8.125 77.861 2000 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.24), residues: 1254 helix: -0.96 (0.36), residues: 178 sheet: -0.48 (0.36), residues: 176 loop : -2.04 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 551 HIS 0.003 0.001 HIS B 100 PHE 0.033 0.002 PHE B 96 TYR 0.026 0.002 TYR K 19 ARG 0.003 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.90227 ( 36) link_BETA1-4 : bond 0.00332 ( 10) link_BETA1-4 : angle 2.35758 ( 30) hydrogen bonds : bond 0.04111 ( 226) hydrogen bonds : angle 7.09634 ( 588) link_BETA1-6 : bond 0.00333 ( 6) link_BETA1-6 : angle 1.47332 ( 18) SS BOND : bond 0.00305 ( 30) SS BOND : angle 1.34245 ( 60) covalent geometry : bond 0.00386 (11022) covalent geometry : angle 0.71040 (14922) *********************** 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 112 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.314 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: 0.9163 (mt0) cc_final: 0.8910 (mt0) REVERT: A 81 VAL cc_start: 0.9637 (t) cc_final: 0.9371 (t) REVERT: A 110 MET cc_start: 0.8619 (mmp) cc_final: 0.8302 (mmm) REVERT: A 294 MET cc_start: 0.8248 (ppp) cc_final: 0.7683 (ppp) REVERT: A 322 ASP cc_start: 0.9239 (p0) cc_final: 0.8888 (p0) REVERT: A 442 MET cc_start: 0.9566 (ttt) cc_final: 0.9105 (tmm) REVERT: A 504 MET cc_start: 0.9100 (mmm) cc_final: 0.8869 (mmm) REVERT: A 551 TRP cc_start: 0.9393 (t-100) cc_final: 0.8955 (t-100) REVERT: B 34 GLN cc_start: 0.9305 (mt0) cc_final: 0.9011 (mt0) REVERT: B 54 LEU cc_start: 0.9471 (tp) cc_final: 0.9217 (tp) REVERT: B 101 LEU cc_start: 0.9732 (tp) cc_final: 0.9497 (mt) REVERT: B 294 MET cc_start: 0.8524 (ppp) cc_final: 0.8025 (ppp) REVERT: B 322 ASP cc_start: 0.9285 (p0) cc_final: 0.8982 (p0) REVERT: B 442 MET cc_start: 0.9593 (ttt) cc_final: 0.9087 (tpt) REVERT: B 479 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7982 (ttp80) REVERT: B 486 LEU cc_start: 0.9665 (tp) cc_final: 0.8978 (mt) REVERT: B 504 MET cc_start: 0.9312 (mmp) cc_final: 0.8975 (mmm) REVERT: B 553 MET cc_start: 0.8925 (tpp) cc_final: 0.8572 (tpp) REVERT: M 703 LYS cc_start: 0.9440 (tptm) cc_final: 0.9102 (tptm) REVERT: M 706 GLU cc_start: 0.9158 (tp30) cc_final: 0.8614 (tp30) REVERT: O 13 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9256 (mm-30) REVERT: P 697 GLU cc_start: 0.9147 (tt0) cc_final: 0.8436 (pp20) REVERT: P 703 LYS cc_start: 0.9397 (tptm) cc_final: 0.9133 (tptm) REVERT: P 706 GLU cc_start: 0.9370 (tp30) cc_final: 0.8994 (tp30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2316 time to fit residues: 37.4828 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 : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.045618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033996 restraints weight = 65007.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.035255 restraints weight = 43527.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.036231 restraints weight = 32645.535| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11080 Z= 0.188 Angle : 0.732 8.239 15066 Z= 0.357 Chirality : 0.046 0.231 1720 Planarity : 0.005 0.060 1876 Dihedral : 7.861 75.852 2000 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.24), residues: 1254 helix: -0.98 (0.36), residues: 178 sheet: -0.49 (0.36), residues: 176 loop : -2.00 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.004 0.001 HIS A 100 PHE 0.052 0.002 PHE P 714 TYR 0.028 0.002 TYR N 19 ARG 0.003 0.000 ARG A 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 12) link_NAG-ASN : angle 2.88705 ( 36) link_BETA1-4 : bond 0.00373 ( 10) link_BETA1-4 : angle 2.23182 ( 30) hydrogen bonds : bond 0.04118 ( 226) hydrogen bonds : angle 6.98403 ( 588) link_BETA1-6 : bond 0.00328 ( 6) link_BETA1-6 : angle 1.48401 ( 18) SS BOND : bond 0.00272 ( 30) SS BOND : angle 1.29496 ( 60) covalent geometry : bond 0.00400 (11022) covalent geometry : angle 0.70807 (14922) *********************** 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 : 1.259 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: 0.9331 (mt0) cc_final: 0.9070 (mt0) REVERT: A 81 VAL cc_start: 0.9643 (t) cc_final: 0.9309 (t) REVERT: A 98 MET cc_start: 0.8516 (mmp) cc_final: 0.8306 (mmm) REVERT: A 109 LEU cc_start: 0.9747 (tp) cc_final: 0.9544 (tp) REVERT: A 110 MET cc_start: 0.8611 (mmp) cc_final: 0.8310 (mmm) REVERT: A 322 ASP cc_start: 0.9209 (p0) cc_final: 0.8848 (p0) REVERT: A 442 MET cc_start: 0.9589 (ttt) cc_final: 0.9207 (tmm) REVERT: A 479 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7908 (ttp80) REVERT: A 486 LEU cc_start: 0.9702 (tp) cc_final: 0.9036 (tp) REVERT: A 504 MET cc_start: 0.9017 (mmm) cc_final: 0.8744 (mmm) REVERT: A 551 TRP cc_start: 0.9361 (t-100) cc_final: 0.8899 (t-100) REVERT: B 54 LEU cc_start: 0.9482 (tp) cc_final: 0.9234 (tp) REVERT: B 98 MET cc_start: 0.8754 (mmm) cc_final: 0.7794 (mmm) REVERT: B 101 LEU cc_start: 0.9748 (tp) cc_final: 0.9451 (mt) REVERT: B 357 ASN cc_start: 0.9056 (p0) cc_final: 0.8826 (t0) REVERT: B 442 MET cc_start: 0.9604 (ttt) cc_final: 0.9103 (tpt) REVERT: B 479 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7936 (ttp80) REVERT: B 486 LEU cc_start: 0.9684 (tp) cc_final: 0.8934 (mt) REVERT: B 504 MET cc_start: 0.9334 (mmp) cc_final: 0.8947 (mmm) REVERT: B 553 MET cc_start: 0.8970 (tpp) cc_final: 0.8609 (tpp) REVERT: M 695 GLU cc_start: 0.9067 (mp0) cc_final: 0.8803 (mp0) REVERT: M 703 LYS cc_start: 0.9436 (tptm) cc_final: 0.9078 (tptm) REVERT: M 706 GLU cc_start: 0.9173 (tp30) cc_final: 0.8591 (tp30) REVERT: O 13 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9250 (mm-30) REVERT: P 697 GLU cc_start: 0.9177 (tt0) cc_final: 0.8520 (pp20) REVERT: P 703 LYS cc_start: 0.9406 (tptm) cc_final: 0.9139 (tptm) REVERT: P 706 GLU cc_start: 0.9431 (tp30) cc_final: 0.8993 (tp30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2107 time to fit residues: 33.8427 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 : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 84 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** 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 431 ASN P 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.045275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.033679 restraints weight = 65326.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034948 restraints weight = 43502.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035904 restraints weight = 32424.488| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11080 Z= 0.193 Angle : 0.729 7.543 15066 Z= 0.356 Chirality : 0.046 0.231 1720 Planarity : 0.005 0.058 1876 Dihedral : 7.737 73.185 2000 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1254 helix: -1.13 (0.36), residues: 176 sheet: -0.52 (0.36), residues: 176 loop : -1.96 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.004 0.001 HIS B 100 PHE 0.041 0.002 PHE P 714 TYR 0.028 0.002 TYR N 19 ARG 0.003 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 2.86610 ( 36) link_BETA1-4 : bond 0.00398 ( 10) link_BETA1-4 : angle 2.18403 ( 30) hydrogen bonds : bond 0.03955 ( 226) hydrogen bonds : angle 6.90463 ( 588) link_BETA1-6 : bond 0.00310 ( 6) link_BETA1-6 : angle 1.50454 ( 18) SS BOND : bond 0.00491 ( 30) SS BOND : angle 1.14188 ( 60) covalent geometry : bond 0.00412 (11022) covalent geometry : angle 0.70609 (14922) *********************** 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 101 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9214 (mt0) cc_final: 0.8916 (mt0) REVERT: A 81 VAL cc_start: 0.9647 (t) cc_final: 0.9281 (t) REVERT: A 109 LEU cc_start: 0.9756 (tp) cc_final: 0.9555 (tp) REVERT: A 110 MET cc_start: 0.8593 (mmp) cc_final: 0.8283 (mmm) REVERT: A 322 ASP cc_start: 0.9149 (p0) cc_final: 0.8795 (p0) REVERT: A 442 MET cc_start: 0.9609 (ttt) cc_final: 0.9239 (tmm) REVERT: A 486 LEU cc_start: 0.9736 (tp) cc_final: 0.9239 (tp) REVERT: A 504 MET cc_start: 0.9020 (mmm) cc_final: 0.8729 (mmm) REVERT: A 553 MET cc_start: 0.9222 (tpt) cc_final: 0.8902 (tpp) REVERT: B 54 LEU cc_start: 0.9520 (tp) cc_final: 0.9283 (tp) REVERT: B 98 MET cc_start: 0.8919 (mmm) cc_final: 0.8317 (mmm) REVERT: B 442 MET cc_start: 0.9609 (ttt) cc_final: 0.9122 (tpt) REVERT: B 486 LEU cc_start: 0.9698 (tp) cc_final: 0.9193 (tp) REVERT: B 504 MET cc_start: 0.9326 (mmp) cc_final: 0.8968 (mmm) REVERT: B 553 MET cc_start: 0.8956 (tpp) cc_final: 0.8498 (tpp) REVERT: M 695 GLU cc_start: 0.9143 (mp0) cc_final: 0.8869 (mp0) REVERT: M 703 LYS cc_start: 0.9425 (tptm) cc_final: 0.9086 (tptm) REVERT: M 706 GLU cc_start: 0.9225 (tp30) cc_final: 0.8614 (tp30) REVERT: O 13 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9218 (mm-30) REVERT: P 697 GLU cc_start: 0.9207 (tt0) cc_final: 0.8592 (pp20) REVERT: P 703 LYS cc_start: 0.9412 (tptm) cc_final: 0.9139 (tptm) REVERT: P 706 GLU cc_start: 0.9443 (tp30) cc_final: 0.8975 (tp30) REVERT: P 720 ARG cc_start: 0.6675 (mmp80) cc_final: 0.6431 (mmp80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2189 time to fit residues: 32.3399 Evaluate side-chains 80 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** P 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.046056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.034308 restraints weight = 65221.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.035669 restraints weight = 42829.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036668 restraints weight = 31594.548| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3897 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 : 0.720 12.347 15066 Z= 0.345 Chirality : 0.046 0.234 1720 Planarity : 0.005 0.057 1876 Dihedral : 8.332 70.323 2000 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1254 helix: -0.98 (0.37), residues: 176 sheet: -0.56 (0.35), residues: 178 loop : -1.91 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 551 HIS 0.003 0.001 HIS L 10 PHE 0.032 0.002 PHE B 96 TYR 0.025 0.001 TYR N 19 ARG 0.011 0.001 ARG A 479 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 12) link_NAG-ASN : angle 3.82835 ( 36) link_BETA1-4 : bond 0.00425 ( 10) link_BETA1-4 : angle 2.11338 ( 30) hydrogen bonds : bond 0.03814 ( 226) hydrogen bonds : angle 6.64516 ( 588) link_BETA1-6 : bond 0.00422 ( 6) link_BETA1-6 : angle 1.37153 ( 18) SS BOND : bond 0.00369 ( 30) SS BOND : angle 1.20703 ( 60) covalent geometry : bond 0.00290 (11022) covalent geometry : angle 0.68629 (14922) *********************** 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 : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9277 (mt0) cc_final: 0.8993 (mt0) REVERT: A 81 VAL cc_start: 0.9627 (t) cc_final: 0.9230 (t) REVERT: A 101 LEU cc_start: 0.9696 (mt) cc_final: 0.9490 (mm) REVERT: A 109 LEU cc_start: 0.9752 (tp) cc_final: 0.9431 (tp) REVERT: A 110 MET cc_start: 0.8506 (mmp) cc_final: 0.8154 (mmm) REVERT: A 322 ASP cc_start: 0.9094 (p0) cc_final: 0.8724 (p0) REVERT: A 442 MET cc_start: 0.9565 (ttt) cc_final: 0.9189 (tmm) REVERT: A 504 MET cc_start: 0.8979 (mmm) cc_final: 0.8704 (mmm) REVERT: A 553 MET cc_start: 0.9116 (tpt) cc_final: 0.8842 (tpt) REVERT: B 34 GLN cc_start: 0.9339 (mt0) cc_final: 0.9027 (mt0) REVERT: B 54 LEU cc_start: 0.9515 (tp) cc_final: 0.9300 (tp) REVERT: B 98 MET cc_start: 0.8692 (mmm) cc_final: 0.8230 (mmm) REVERT: B 101 LEU cc_start: 0.9633 (mt) cc_final: 0.9374 (mm) REVERT: B 442 MET cc_start: 0.9557 (ttt) cc_final: 0.9084 (tpt) REVERT: B 504 MET cc_start: 0.9275 (mmp) cc_final: 0.8895 (mmm) REVERT: B 553 MET cc_start: 0.8878 (tpp) cc_final: 0.8459 (tpp) REVERT: M 695 GLU cc_start: 0.9100 (mp0) cc_final: 0.8872 (mp0) REVERT: M 703 LYS cc_start: 0.9412 (tptm) cc_final: 0.9058 (tptm) REVERT: M 706 GLU cc_start: 0.9116 (tp30) cc_final: 0.8539 (tp30) REVERT: O 13 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9215 (mm-30) REVERT: P 697 GLU cc_start: 0.9193 (tt0) cc_final: 0.8597 (pp20) REVERT: P 703 LYS cc_start: 0.9427 (tptm) cc_final: 0.9138 (tptm) REVERT: P 706 GLU cc_start: 0.9366 (tp30) cc_final: 0.8930 (tp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1914 time to fit residues: 31.3490 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 : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.046411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034667 restraints weight = 62415.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035998 restraints weight = 41524.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037005 restraints weight = 30797.765| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11080 Z= 0.115 Angle : 0.687 11.628 15066 Z= 0.332 Chirality : 0.046 0.231 1720 Planarity : 0.004 0.054 1876 Dihedral : 8.252 77.818 2000 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1254 helix: -0.83 (0.37), residues: 176 sheet: -0.51 (0.35), residues: 178 loop : -1.88 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 551 HIS 0.003 0.001 HIS L 5 PHE 0.037 0.002 PHE B 96 TYR 0.023 0.001 TYR N 19 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 2.70798 ( 36) link_BETA1-4 : bond 0.00444 ( 10) link_BETA1-4 : angle 2.05951 ( 30) hydrogen bonds : bond 0.03676 ( 226) hydrogen bonds : angle 6.57229 ( 588) link_BETA1-6 : bond 0.00590 ( 6) link_BETA1-6 : angle 1.29261 ( 18) SS BOND : bond 0.00317 ( 30) SS BOND : angle 1.01687 ( 60) covalent geometry : bond 0.00251 (11022) covalent geometry : angle 0.66679 (14922) *********************** 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 102 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9303 (mt0) cc_final: 0.9074 (mt0) REVERT: A 81 VAL cc_start: 0.9618 (t) cc_final: 0.9200 (t) REVERT: A 87 LEU cc_start: 0.9166 (mt) cc_final: 0.8901 (tp) REVERT: A 109 LEU cc_start: 0.9759 (tp) cc_final: 0.9424 (tp) REVERT: A 110 MET cc_start: 0.8528 (mmp) cc_final: 0.8173 (mmm) REVERT: A 442 MET cc_start: 0.9587 (ttt) cc_final: 0.9199 (tmm) REVERT: A 473 LEU cc_start: 0.9269 (mt) cc_final: 0.9062 (mt) REVERT: A 504 MET cc_start: 0.8976 (mmm) cc_final: 0.8708 (mmm) REVERT: A 553 MET cc_start: 0.9244 (tpt) cc_final: 0.9040 (tpp) REVERT: B 34 GLN cc_start: 0.9372 (mt0) cc_final: 0.9060 (mt0) REVERT: B 54 LEU cc_start: 0.9524 (tp) cc_final: 0.9322 (tp) REVERT: B 87 LEU cc_start: 0.9133 (mt) cc_final: 0.8852 (tp) REVERT: B 98 MET cc_start: 0.8743 (mmm) cc_final: 0.8285 (mmm) REVERT: B 101 LEU cc_start: 0.9629 (mt) cc_final: 0.9355 (mm) REVERT: B 442 MET cc_start: 0.9573 (ttt) cc_final: 0.9096 (tpt) REVERT: B 504 MET cc_start: 0.9279 (mmp) cc_final: 0.8901 (mmm) REVERT: B 553 MET cc_start: 0.8924 (tpp) cc_final: 0.8563 (tpp) REVERT: M 695 GLU cc_start: 0.9130 (mp0) cc_final: 0.8929 (mp0) REVERT: M 703 LYS cc_start: 0.9382 (tptm) cc_final: 0.9170 (tptp) REVERT: O 13 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9276 (mm-30) REVERT: P 697 GLU cc_start: 0.9185 (tt0) cc_final: 0.8595 (pp20) REVERT: P 703 LYS cc_start: 0.9393 (tptm) cc_final: 0.9091 (tptm) REVERT: P 706 GLU cc_start: 0.9443 (tp30) cc_final: 0.8939 (tp30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2005 time to fit residues: 31.3253 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 : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.0470 chunk 70 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.047124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.035336 restraints weight = 64140.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036685 restraints weight = 42403.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.037520 restraints weight = 31390.763| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11080 Z= 0.105 Angle : 0.686 11.807 15066 Z= 0.332 Chirality : 0.047 0.228 1720 Planarity : 0.004 0.053 1876 Dihedral : 7.680 70.175 2000 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1254 helix: -0.89 (0.38), residues: 174 sheet: -0.43 (0.35), residues: 178 loop : -1.80 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 559 HIS 0.003 0.001 HIS L 5 PHE 0.034 0.001 PHE B 96 TYR 0.020 0.001 TYR N 19 ARG 0.004 0.000 ARG A 14 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 2.72433 ( 36) link_BETA1-4 : bond 0.00454 ( 10) link_BETA1-4 : angle 2.01656 ( 30) hydrogen bonds : bond 0.03630 ( 226) hydrogen bonds : angle 6.34906 ( 588) link_BETA1-6 : bond 0.00543 ( 6) link_BETA1-6 : angle 1.23494 ( 18) SS BOND : bond 0.00284 ( 30) SS BOND : angle 0.94352 ( 60) covalent geometry : bond 0.00229 (11022) covalent geometry : angle 0.66578 (14922) *********************** 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 106 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.243 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: 0.9340 (mt0) cc_final: 0.9094 (mt0) REVERT: A 38 MET cc_start: 0.8865 (mmt) cc_final: 0.8544 (mmt) REVERT: A 81 VAL cc_start: 0.9608 (t) cc_final: 0.9142 (t) REVERT: A 87 LEU cc_start: 0.9147 (mt) cc_final: 0.8886 (tp) REVERT: A 101 LEU cc_start: 0.9688 (mt) cc_final: 0.9458 (mm) REVERT: A 109 LEU cc_start: 0.9763 (tp) cc_final: 0.9410 (tp) REVERT: A 110 MET cc_start: 0.8532 (mmp) cc_final: 0.8193 (mmm) REVERT: A 442 MET cc_start: 0.9585 (ttt) cc_final: 0.9165 (tmm) REVERT: A 504 MET cc_start: 0.8995 (mmm) cc_final: 0.8734 (mmm) REVERT: B 38 MET cc_start: 0.8951 (mmt) cc_final: 0.8639 (mmt) REVERT: B 87 LEU cc_start: 0.9085 (mt) cc_final: 0.8832 (tp) REVERT: B 98 MET cc_start: 0.8752 (mmm) cc_final: 0.8305 (mmm) REVERT: B 442 MET cc_start: 0.9587 (ttt) cc_final: 0.9131 (tpt) REVERT: B 504 MET cc_start: 0.9296 (mmp) cc_final: 0.8932 (mmm) REVERT: M 703 LYS cc_start: 0.9387 (tptm) cc_final: 0.9179 (tptp) REVERT: M 706 GLU cc_start: 0.9079 (tp30) cc_final: 0.8806 (tp30) REVERT: O 13 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9314 (mm-30) REVERT: P 697 GLU cc_start: 0.9159 (tt0) cc_final: 0.8553 (pp20) REVERT: P 703 LYS cc_start: 0.9390 (tptm) cc_final: 0.9097 (tptm) REVERT: P 706 GLU cc_start: 0.9333 (tp30) cc_final: 0.8859 (tp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2096 time to fit residues: 33.1235 Evaluate side-chains 91 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** 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 = 0.3126 r_free = 0.3126 target = 0.046894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.035085 restraints weight = 64342.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036435 restraints weight = 42334.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037340 restraints weight = 31342.378| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11080 Z= 0.111 Angle : 0.698 11.756 15066 Z= 0.337 Chirality : 0.047 0.270 1720 Planarity : 0.004 0.051 1876 Dihedral : 7.297 63.988 2000 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1254 helix: -0.87 (0.38), residues: 174 sheet: -0.20 (0.36), residues: 172 loop : -1.83 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 551 HIS 0.003 0.001 HIS L 5 PHE 0.023 0.002 PHE B 96 TYR 0.024 0.001 TYR K 14 ARG 0.003 0.000 ARG A 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 12) link_NAG-ASN : angle 2.86993 ( 36) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 1.95232 ( 30) hydrogen bonds : bond 0.03719 ( 226) hydrogen bonds : angle 6.27807 ( 588) link_BETA1-6 : bond 0.00467 ( 6) link_BETA1-6 : angle 1.25774 ( 18) SS BOND : bond 0.00299 ( 30) SS BOND : angle 1.00913 ( 60) covalent geometry : bond 0.00247 (11022) covalent geometry : angle 0.67714 (14922) ********************** 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 105 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.340 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: 0.9299 (mt0) cc_final: 0.9011 (mt0) REVERT: A 38 MET cc_start: 0.9095 (mmt) cc_final: 0.8738 (mmt) REVERT: A 87 LEU cc_start: 0.9135 (mt) cc_final: 0.8905 (tp) REVERT: A 108 ASN cc_start: 0.9392 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: A 109 LEU cc_start: 0.9756 (tp) cc_final: 0.9431 (tp) REVERT: A 110 MET cc_start: 0.8515 (mmp) cc_final: 0.8191 (mmm) REVERT: A 442 MET cc_start: 0.9562 (ttt) cc_final: 0.9169 (tmm) REVERT: A 504 MET cc_start: 0.8950 (mmm) cc_final: 0.8703 (mmm) REVERT: B 87 LEU cc_start: 0.9104 (mt) cc_final: 0.8861 (tp) REVERT: B 98 MET cc_start: 0.8802 (mmm) cc_final: 0.8263 (mmm) REVERT: B 442 MET cc_start: 0.9576 (ttt) cc_final: 0.9133 (tpt) REVERT: B 553 MET cc_start: 0.8912 (tpp) cc_final: 0.8544 (tpp) REVERT: B 574 ASP cc_start: 0.9461 (p0) cc_final: 0.9108 (m-30) REVERT: M 706 GLU cc_start: 0.8967 (tp30) cc_final: 0.8687 (tp30) REVERT: O 13 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9324 (mm-30) REVERT: P 697 GLU cc_start: 0.9129 (tt0) cc_final: 0.8541 (pp20) REVERT: P 703 LYS cc_start: 0.9396 (tptm) cc_final: 0.9112 (tptm) REVERT: P 706 GLU cc_start: 0.9415 (tp30) cc_final: 0.8873 (tp30) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2055 time to fit residues: 32.4330 Evaluate side-chains 91 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 0.1980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.046176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.034544 restraints weight = 64362.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035788 restraints weight = 42793.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036749 restraints weight = 32156.708| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11080 Z= 0.148 Angle : 0.711 11.548 15066 Z= 0.343 Chirality : 0.046 0.239 1720 Planarity : 0.004 0.053 1876 Dihedral : 6.990 58.314 2000 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % 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 : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.24), residues: 1254 helix: -0.95 (0.38), residues: 174 sheet: -0.12 (0.36), residues: 170 loop : -1.84 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.003 0.001 HIS L 5 PHE 0.035 0.002 PHE B 96 TYR 0.019 0.001 TYR N 19 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 12) link_NAG-ASN : angle 3.01665 ( 36) link_BETA1-4 : bond 0.00388 ( 10) link_BETA1-4 : angle 1.97557 ( 30) hydrogen bonds : bond 0.03529 ( 226) hydrogen bonds : angle 6.39608 ( 588) link_BETA1-6 : bond 0.00335 ( 6) link_BETA1-6 : angle 1.38714 ( 18) SS BOND : bond 0.00282 ( 30) SS BOND : angle 1.05859 ( 60) covalent geometry : bond 0.00325 (11022) covalent geometry : angle 0.68828 (14922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.02 seconds wall clock time: 51 minutes 43.52 seconds (3103.52 seconds total)