Starting phenix.real_space_refine on Thu Sep 18 03:20:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.map" model { file = "/net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bp7_44763/09_2025/9bp7_44763.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.105 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 93 5.16 5 C 8966 2.51 5 N 2196 2.21 5 O 2476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13731 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2751 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 343, 2751 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2812 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2734 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2728 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2765 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2659 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 192 " occ=0.79 ... (16 atoms not shown) pdb=" OE2BGLU A 192 " occ=0.21 Time building chain proxies: 3.67, per 1000 atoms: 0.27 Number of scatterers: 13731 At special positions: 0 Unit cell: (89.64, 92.13, 137.78, 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 93 16.00 O 2476 8.00 N 2196 7.00 C 8966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 731.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 39.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.717A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.010A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 241 removed outlier: 4.547A pdb=" N ILE A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.903A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 248 through 272 removed outlier: 3.598A pdb=" N VAL A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 309 Processing helix chain 'A' and resid 388 through 420 Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 20 through 23 removed outlier: 3.700A pdb=" N GLY B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 71 through 74 removed outlier: 4.059A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.778A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 239 removed outlier: 3.726A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.815A pdb=" N TRP B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 4.164A pdb=" N TRP B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.606A pdb=" N ILE B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 Processing helix chain 'B' and resid 387 through 420 Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.690A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.805A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 243 removed outlier: 4.035A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.782A pdb=" N SER C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 267 removed outlier: 3.898A pdb=" N ARG C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 Processing helix chain 'C' and resid 388 through 420 Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.948A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.758A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 239 removed outlier: 3.593A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.713A pdb=" N TRP D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 4.148A pdb=" N TRP D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.514A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 Processing helix chain 'D' and resid 388 through 420 Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 109 through 116 removed outlier: 3.847A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 116 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 245 through 264 removed outlier: 4.075A pdb=" N MET E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Proline residue: E 254 - end of helix Processing helix chain 'E' and resid 265 through 268 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 275 through 295 removed outlier: 3.836A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 295 " --> pdb=" O CYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 332 Processing helix chain 'E' and resid 446 through 474 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 52 removed outlier: 6.576A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 44 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 69 current: chain 'A' and resid 125 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 157 current: chain 'A' and resid 209 through 218 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 47 removed outlier: 3.778A pdb=" N PHE B 44 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 69 current: chain 'B' and resid 125 through 137 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 149 through 157 current: chain 'B' and resid 209 through 218 Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 52 removed outlier: 6.346A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 69 current: chain 'C' and resid 125 through 137 Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 149 through 157 current: chain 'C' and resid 209 through 218 Processing sheet with id=AA8, first strand: chain 'D' and resid 37 through 52 removed outlier: 6.557A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 69 current: chain 'D' and resid 125 through 137 Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 157 removed outlier: 4.660A pdb=" N HIS D 215 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU D 192 " --> pdb=" O HIS D 215 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLU D 217 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS D 190 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 73 removed outlier: 6.456A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 90 current: chain 'E' and resid 148 through 156 Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.581A pdb=" N GLY E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.668A pdb=" N ARG E 241 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 210 " --> pdb=" O ARG E 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 224 through 225 512 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 3019 1.45 - 1.58: 7441 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14083 Sorted by residual: bond pdb=" N PRO A 250 " pdb=" CD PRO A 250 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.26e+00 bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.26e+00 bond pdb=" N ILE E 139 " pdb=" CA ILE E 139 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N MET C 246 " pdb=" CA MET C 246 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.07e+00 bond pdb=" N ARG B 252 " pdb=" CA ARG B 252 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.86e+00 ... (remaining 14078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 18787 1.46 - 2.93: 256 2.93 - 4.39: 82 4.39 - 5.86: 28 5.86 - 7.32: 2 Bond angle restraints: 19155 Sorted by residual: angle pdb=" CA ILE E 139 " pdb=" C ILE E 139 " pdb=" O ILE E 139 " ideal model delta sigma weight residual 120.43 117.16 3.27 1.09e+00 8.42e-01 9.00e+00 angle pdb=" C LYS D 419 " pdb=" N ILE D 420 " pdb=" CA ILE D 420 " ideal model delta sigma weight residual 122.97 120.05 2.92 9.80e-01 1.04e+00 8.89e+00 angle pdb=" C VAL C 111 " pdb=" N THR C 112 " pdb=" CA THR C 112 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.97e+00 angle pdb=" C VAL D 111 " pdb=" N THR D 112 " pdb=" CA THR D 112 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.85e+00 angle pdb=" C VAL B 111 " pdb=" N THR B 112 " pdb=" CA THR B 112 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.20e+00 ... (remaining 19150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 7886 17.26 - 34.53: 436 34.53 - 51.79: 98 51.79 - 69.05: 8 69.05 - 86.32: 3 Dihedral angle restraints: 8431 sinusoidal: 3375 harmonic: 5056 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -158.25 72.25 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CA ILE D 420 " pdb=" C ILE D 420 " pdb=" N LEU D 421 " pdb=" CA LEU D 421 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA MET C 227 " pdb=" C MET C 227 " pdb=" N TYR C 228 " pdb=" CA TYR C 228 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1863 0.056 - 0.112: 293 0.112 - 0.168: 23 0.168 - 0.224: 4 0.224 - 0.280: 2 Chirality restraints: 2185 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE E 139 " pdb=" N ILE E 139 " pdb=" C ILE E 139 " pdb=" CB ILE E 139 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 NAG B 501 " pdb=" C1 NAG B 501 " pdb=" C3 NAG B 501 " pdb=" N2 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2182 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 249 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 250 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 224 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C LEU B 224 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU B 224 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 225 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 224 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU A 224 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU A 224 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE A 225 " -0.008 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 66 2.52 - 3.11: 10177 3.11 - 3.71: 20475 3.71 - 4.30: 27423 4.30 - 4.90: 47435 Nonbonded interactions: 105576 Sorted by model distance: nonbonded pdb=" O PRO E 278 " pdb=" CD2 PHE E 282 " model vdw 1.924 3.340 nonbonded pdb=" CD1 LEU A 255 " pdb=" CD1 ILE E 281 " model vdw 1.983 3.880 nonbonded pdb=" CE MET C 246 " pdb=" CG1 VAL C 304 " model vdw 2.083 3.880 nonbonded pdb=" O ALA A 254 " pdb=" OG1 THR A 258 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR A 112 " pdb=" O LEU E 121 " model vdw 2.154 3.040 ... (remaining 105571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 191 or resid 193 through 310 or resid 386 throug \ h 395 or (resid 396 through 401 and (name N or name CA or name C or name O or na \ me CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'B' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ id 386 through 387 or (resid 388 and (name N or name CA or name C or name O or n \ ame CB )) or resid 389 through 392 or (resid 393 and (name N or name CA or name \ C or name O or name CB )) or resid 394 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 387 or (re \ sid 388 and (name N or name CA or name C or name O or name CB )) or resid 389 th \ rough 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) \ or resid 394 through 396 or (resid 397 through 401 and (name N or name CA or na \ me C or name O or name CB )) or resid 402 through 422)) selection = (chain 'D' and (resid 9 through 191 or resid 193 through 387 or (resid 388 and ( \ name N or name CA or name C or name O or name CB )) or resid 389 through 392 or \ (resid 393 and (name N or name CA or name C or name O or name CB )) or resid 394 \ through 396 or (resid 397 through 401 and (name N or name CA or name C or name \ O or name CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or \ name C or name O or name CB )))) } 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=0.21 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: 1.550 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.860 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0500 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 : 0.003 0.040 14098 Z= 0.132 Angle : 0.540 7.402 19190 Z= 0.277 Chirality : 0.042 0.280 2185 Planarity : 0.003 0.050 2395 Dihedral : 10.982 86.319 5115 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.38 % Rotamer: Outliers : 3.55 % Allowed : 7.04 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1686 helix: 2.50 (0.22), residues: 571 sheet: -0.68 (0.27), residues: 386 loop : -1.23 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 131 TYR 0.013 0.001 TYR C 414 PHE 0.010 0.001 PHE C 48 TRP 0.007 0.001 TRP C 415 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00263 (14083) covalent geometry : angle 0.52986 (19155) SS BOND : bond 0.00152 ( 10) SS BOND : angle 0.54946 ( 20) hydrogen bonds : bond 0.14316 ( 512) hydrogen bonds : angle 6.30867 ( 1449) link_NAG-ASN : bond 0.00447 ( 5) link_NAG-ASN : angle 3.67425 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TYR cc_start: 0.2246 (t80) cc_final: 0.2024 (t80) REVERT: B 264 THR cc_start: 0.4766 (m) cc_final: 0.4468 (m) REVERT: C 198 CYS cc_start: 0.2218 (OUTLIER) cc_final: 0.0029 (t) REVERT: C 219 GLN cc_start: 0.2146 (OUTLIER) cc_final: 0.1596 (pt0) REVERT: C 287 MET cc_start: 0.3960 (mmt) cc_final: 0.2123 (ptt) REVERT: D 287 MET cc_start: 0.2700 (mmt) cc_final: 0.1958 (ptt) REVERT: E 76 THR cc_start: 0.4715 (OUTLIER) cc_final: 0.4502 (m) outliers start: 53 outliers final: 16 residues processed: 248 average time/residue: 0.1076 time to fit residues: 41.1299 Evaluate side-chains 162 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 203 ASN C 219 GLN D 177 GLN E 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.193479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161482 restraints weight = 43457.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168744 restraints weight = 17176.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.172173 restraints weight = 7851.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.172444 restraints weight = 5519.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173282 restraints weight = 5057.435| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1100 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14098 Z= 0.147 Angle : 0.670 10.422 19190 Z= 0.331 Chirality : 0.045 0.246 2185 Planarity : 0.004 0.059 2395 Dihedral : 6.351 74.361 1972 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.62 % Favored : 96.14 % Rotamer: Outliers : 2.41 % Allowed : 11.53 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.21), residues: 1686 helix: 2.33 (0.22), residues: 554 sheet: -0.56 (0.27), residues: 400 loop : -1.16 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 252 TYR 0.017 0.001 TYR A 279 PHE 0.012 0.001 PHE E 131 TRP 0.025 0.001 TRP E 263 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00311 (14083) covalent geometry : angle 0.65810 (19155) SS BOND : bond 0.01523 ( 10) SS BOND : angle 1.33683 ( 20) hydrogen bonds : bond 0.03937 ( 512) hydrogen bonds : angle 5.23810 ( 1449) link_NAG-ASN : bond 0.01097 ( 5) link_NAG-ASN : angle 4.37825 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4928 (mp) cc_final: 0.4376 (mm) REVERT: A 163 MET cc_start: -0.0530 (mtt) cc_final: -0.1463 (tpt) REVERT: B 198 CYS cc_start: -0.0136 (OUTLIER) cc_final: -0.2192 (m) REVERT: C 287 MET cc_start: 0.4306 (mmt) cc_final: 0.2182 (ptt) REVERT: D 111 VAL cc_start: 0.2716 (OUTLIER) cc_final: 0.1950 (m) REVERT: D 163 MET cc_start: 0.3879 (mmt) cc_final: 0.2099 (ppp) REVERT: D 246 MET cc_start: 0.4618 (mmm) cc_final: 0.3999 (tpt) REVERT: D 287 MET cc_start: 0.3200 (mmt) cc_final: 0.2039 (ptt) REVERT: E 212 LYS cc_start: 0.5657 (OUTLIER) cc_final: 0.4654 (ptpp) outliers start: 36 outliers final: 20 residues processed: 184 average time/residue: 0.1134 time to fit residues: 31.5423 Evaluate side-chains 155 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 46 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.198906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167918 restraints weight = 34064.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174082 restraints weight = 14290.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177883 restraints weight = 7793.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180334 restraints weight = 5159.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181688 restraints weight = 3931.615| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1310 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14098 Z= 0.125 Angle : 0.634 8.853 19190 Z= 0.309 Chirality : 0.044 0.257 2185 Planarity : 0.004 0.034 2395 Dihedral : 6.055 69.202 1959 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.03 % Favored : 96.73 % Rotamer: Outliers : 2.82 % Allowed : 11.86 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.21), residues: 1686 helix: 2.13 (0.22), residues: 561 sheet: -0.58 (0.26), residues: 399 loop : -1.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 213 TYR 0.031 0.001 TYR C 222 PHE 0.027 0.001 PHE C 214 TRP 0.025 0.001 TRP E 263 HIS 0.005 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00259 (14083) covalent geometry : angle 0.62040 (19155) SS BOND : bond 0.00291 ( 10) SS BOND : angle 1.56672 ( 20) hydrogen bonds : bond 0.03532 ( 512) hydrogen bonds : angle 4.96152 ( 1449) link_NAG-ASN : bond 0.00904 ( 5) link_NAG-ASN : angle 4.32386 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.5322 (mp) cc_final: 0.4768 (mm) REVERT: B 198 CYS cc_start: 0.0322 (OUTLIER) cc_final: -0.2380 (m) REVERT: C 56 MET cc_start: 0.1464 (mmm) cc_final: 0.1025 (mmt) REVERT: D 111 VAL cc_start: 0.2816 (OUTLIER) cc_final: 0.1963 (m) REVERT: D 287 MET cc_start: 0.3257 (mmt) cc_final: 0.1920 (ptt) REVERT: E 261 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.3775 (tt) outliers start: 42 outliers final: 25 residues processed: 179 average time/residue: 0.1059 time to fit residues: 29.4426 Evaluate side-chains 156 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 94 optimal weight: 0.0040 chunk 150 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.203866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172512 restraints weight = 40565.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179138 restraints weight = 16257.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183337 restraints weight = 8563.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186017 restraints weight = 5477.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.187729 restraints weight = 4039.033| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1586 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14098 Z= 0.120 Angle : 0.628 12.555 19190 Z= 0.304 Chirality : 0.044 0.224 2185 Planarity : 0.004 0.066 2395 Dihedral : 6.145 66.435 1959 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.85 % Favored : 96.91 % Rotamer: Outliers : 2.75 % Allowed : 13.00 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1686 helix: 1.97 (0.23), residues: 564 sheet: -0.52 (0.27), residues: 398 loop : -1.13 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 271 TYR 0.046 0.001 TYR D 301 PHE 0.029 0.001 PHE A 295 TRP 0.037 0.001 TRP D 239 HIS 0.015 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00255 (14083) covalent geometry : angle 0.61805 (19155) SS BOND : bond 0.00247 ( 10) SS BOND : angle 1.47045 ( 20) hydrogen bonds : bond 0.03212 ( 512) hydrogen bonds : angle 4.82962 ( 1449) link_NAG-ASN : bond 0.00703 ( 5) link_NAG-ASN : angle 3.75091 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4609 (mpp) cc_final: 0.2901 (ttp) REVERT: A 51 ILE cc_start: 0.5564 (mp) cc_final: 0.4980 (mm) REVERT: A 154 MET cc_start: 0.1098 (tpp) cc_final: 0.0730 (mpp) REVERT: A 163 MET cc_start: -0.0703 (mtt) cc_final: -0.1596 (tpt) REVERT: B 18 MET cc_start: 0.2608 (tpp) cc_final: 0.2259 (tpp) REVERT: B 198 CYS cc_start: 0.1399 (OUTLIER) cc_final: -0.1177 (m) REVERT: C 56 MET cc_start: 0.1375 (mmm) cc_final: 0.1120 (mmt) REVERT: C 228 TYR cc_start: 0.3864 (m-10) cc_final: 0.3524 (m-80) REVERT: D 111 VAL cc_start: 0.2994 (OUTLIER) cc_final: 0.2041 (m) REVERT: D 287 MET cc_start: 0.3466 (mmt) cc_final: 0.2127 (ptt) REVERT: E 170 MET cc_start: 0.2912 (tpp) cc_final: 0.2696 (tpp) outliers start: 41 outliers final: 21 residues processed: 184 average time/residue: 0.0949 time to fit residues: 27.7389 Evaluate side-chains 159 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.0000 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 109 HIS E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.205505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176211 restraints weight = 41504.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183665 restraints weight = 16571.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186314 restraints weight = 7946.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187754 restraints weight = 6109.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.188951 restraints weight = 4766.038| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2081 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14098 Z= 0.128 Angle : 0.638 10.973 19190 Z= 0.311 Chirality : 0.044 0.183 2185 Planarity : 0.004 0.052 2395 Dihedral : 5.973 59.058 1956 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.51 % Favored : 96.26 % Rotamer: Outliers : 3.08 % Allowed : 13.61 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1686 helix: 1.92 (0.22), residues: 571 sheet: -0.61 (0.27), residues: 392 loop : -1.09 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.019 0.001 TYR D 301 PHE 0.029 0.001 PHE A 295 TRP 0.034 0.001 TRP D 239 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00280 (14083) covalent geometry : angle 0.62954 (19155) SS BOND : bond 0.00234 ( 10) SS BOND : angle 1.38019 ( 20) hydrogen bonds : bond 0.03166 ( 512) hydrogen bonds : angle 4.66551 ( 1449) link_NAG-ASN : bond 0.00627 ( 5) link_NAG-ASN : angle 3.39743 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.5931 (mp) cc_final: 0.5582 (mp) REVERT: A 163 MET cc_start: -0.0353 (mtt) cc_final: -0.2042 (tpt) REVERT: B 18 MET cc_start: 0.2376 (tpp) cc_final: 0.2160 (tpp) REVERT: B 299 LEU cc_start: 0.7306 (tt) cc_final: 0.6976 (tp) REVERT: C 228 TYR cc_start: 0.4400 (m-10) cc_final: 0.3480 (m-80) REVERT: D 111 VAL cc_start: 0.3451 (OUTLIER) cc_final: 0.2457 (m) REVERT: D 287 MET cc_start: 0.3820 (mmt) cc_final: 0.2256 (mmt) REVERT: E 89 TRP cc_start: 0.2816 (p90) cc_final: 0.1836 (p90) outliers start: 46 outliers final: 31 residues processed: 201 average time/residue: 0.0976 time to fit residues: 31.0176 Evaluate side-chains 173 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 132 optimal weight: 0.0270 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 136 GLN E 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.208903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180764 restraints weight = 32041.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.186609 restraints weight = 14287.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.190361 restraints weight = 8052.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.192749 restraints weight = 5358.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.194311 restraints weight = 4055.381| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4271 r_free = 0.4271 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4271 r_free = 0.4271 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2267 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14098 Z= 0.113 Angle : 0.619 11.937 19190 Z= 0.300 Chirality : 0.042 0.189 2185 Planarity : 0.004 0.047 2395 Dihedral : 6.018 59.992 1956 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.57 % Favored : 96.20 % Rotamer: Outliers : 2.82 % Allowed : 14.75 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1686 helix: 1.93 (0.22), residues: 570 sheet: -0.59 (0.27), residues: 396 loop : -1.06 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.030 0.001 TYR E 325 PHE 0.027 0.001 PHE A 295 TRP 0.029 0.001 TRP D 239 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00237 (14083) covalent geometry : angle 0.61119 (19155) SS BOND : bond 0.00250 ( 10) SS BOND : angle 1.21840 ( 20) hydrogen bonds : bond 0.03017 ( 512) hydrogen bonds : angle 4.60838 ( 1449) link_NAG-ASN : bond 0.00613 ( 5) link_NAG-ASN : angle 3.30825 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.6253 (mp) cc_final: 0.5909 (mp) REVERT: A 163 MET cc_start: -0.0333 (mtt) cc_final: -0.1731 (tpt) REVERT: B 18 MET cc_start: 0.2563 (tpp) cc_final: 0.2231 (tpp) REVERT: C 147 MET cc_start: 0.4540 (mpp) cc_final: 0.3957 (mpp) REVERT: D 111 VAL cc_start: 0.3443 (OUTLIER) cc_final: 0.2505 (m) REVERT: D 227 MET cc_start: 0.5121 (mtt) cc_final: 0.4839 (mtt) REVERT: E 89 TRP cc_start: 0.3335 (p90) cc_final: 0.2045 (p90) outliers start: 42 outliers final: 30 residues processed: 190 average time/residue: 0.0978 time to fit residues: 29.5396 Evaluate side-chains 173 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.0040 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 66 GLN A 115 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 115 ASN C 61 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 201 HIS C 203 ASN D 109 HIS D 215 HIS E 32 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN E 178 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.232870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.205307 restraints weight = 45894.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213766 restraints weight = 18989.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.218665 restraints weight = 8558.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.219235 restraints weight = 5842.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.220274 restraints weight = 4395.570| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 0.9364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 14098 Z= 0.264 Angle : 0.979 32.638 19190 Z= 0.507 Chirality : 0.055 0.499 2185 Planarity : 0.007 0.144 2395 Dihedral : 7.214 59.548 1956 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.06 % Favored : 93.64 % Rotamer: Outliers : 3.42 % Allowed : 15.55 % Favored : 81.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.21), residues: 1686 helix: 1.38 (0.22), residues: 572 sheet: -1.37 (0.27), residues: 375 loop : -1.27 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 65 TYR 0.032 0.003 TYR A 75 PHE 0.050 0.004 PHE B 100 TRP 0.026 0.003 TRP B 239 HIS 0.009 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00569 (14083) covalent geometry : angle 0.97244 (19155) SS BOND : bond 0.01524 ( 10) SS BOND : angle 1.67185 ( 20) hydrogen bonds : bond 0.03832 ( 512) hydrogen bonds : angle 5.02683 ( 1449) link_NAG-ASN : bond 0.00844 ( 5) link_NAG-ASN : angle 3.75881 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.498 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 18 MET cc_start: 0.4790 (mpp) cc_final: 0.2898 (tmm) REVERT: A 62 ILE cc_start: 0.3794 (pt) cc_final: 0.3327 (mt) REVERT: B 18 MET cc_start: 0.2235 (tpp) cc_final: 0.1982 (tpp) REVERT: B 51 ILE cc_start: 0.4515 (mp) cc_final: 0.4107 (mt) REVERT: B 147 MET cc_start: 0.6445 (pmm) cc_final: 0.6014 (pmm) REVERT: B 246 MET cc_start: 0.4496 (pmm) cc_final: 0.2857 (ptp) REVERT: C 147 MET cc_start: 0.6376 (mpp) cc_final: 0.6165 (mpp) REVERT: C 154 MET cc_start: 0.8008 (pmm) cc_final: 0.7228 (ptp) REVERT: C 170 TRP cc_start: 0.6221 (m100) cc_final: 0.5475 (m100) REVERT: D 246 MET cc_start: 0.4081 (mmt) cc_final: 0.3785 (tpt) REVERT: E 89 TRP cc_start: 0.4442 (p90) cc_final: 0.3882 (p90) REVERT: E 199 VAL cc_start: 0.4027 (t) cc_final: 0.2957 (m) REVERT: E 311 LEU cc_start: 0.5569 (mt) cc_final: 0.4898 (mt) outliers start: 51 outliers final: 26 residues processed: 263 average time/residue: 0.1003 time to fit residues: 41.2921 Evaluate side-chains 221 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 201 HIS B 115 ASN C 155 GLN C 219 GLN D 215 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN E 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.225215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197495 restraints weight = 39953.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.204194 restraints weight = 17421.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.208383 restraints weight = 9487.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.211096 restraints weight = 6107.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.212883 restraints weight = 4451.808| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4047 moved from start: 0.9649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14098 Z= 0.134 Angle : 0.714 13.890 19190 Z= 0.344 Chirality : 0.046 0.222 2185 Planarity : 0.004 0.042 2395 Dihedral : 6.391 59.765 1954 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.80 % Favored : 95.96 % Rotamer: Outliers : 2.14 % Allowed : 18.30 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1686 helix: 1.81 (0.23), residues: 564 sheet: -1.16 (0.25), residues: 418 loop : -1.08 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 271 TYR 0.023 0.001 TYR A 222 PHE 0.032 0.001 PHE B 207 TRP 0.018 0.001 TRP D 239 HIS 0.007 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00270 (14083) covalent geometry : angle 0.70587 (19155) SS BOND : bond 0.00607 ( 10) SS BOND : angle 2.03640 ( 20) hydrogen bonds : bond 0.03123 ( 512) hydrogen bonds : angle 4.69458 ( 1449) link_NAG-ASN : bond 0.00667 ( 5) link_NAG-ASN : angle 3.15402 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4689 (mpp) cc_final: 0.2667 (tmm) REVERT: A 75 TYR cc_start: 0.2249 (t80) cc_final: 0.1274 (t80) REVERT: A 163 MET cc_start: -0.0448 (mtt) cc_final: -0.1895 (tpt) REVERT: B 18 MET cc_start: 0.2212 (tpp) cc_final: 0.2002 (tpp) REVERT: B 246 MET cc_start: 0.4203 (pmm) cc_final: 0.2627 (ptp) REVERT: C 147 MET cc_start: 0.6439 (mpp) cc_final: 0.6211 (mpp) REVERT: C 154 MET cc_start: 0.7744 (pmm) cc_final: 0.6697 (ptt) REVERT: D 109 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5678 (t-90) REVERT: D 156 LEU cc_start: 0.5731 (mp) cc_final: 0.5524 (mt) REVERT: D 246 MET cc_start: 0.4100 (mmt) cc_final: 0.3857 (tpt) REVERT: E 89 TRP cc_start: 0.4491 (p90) cc_final: 0.3871 (p90) REVERT: E 177 MET cc_start: 0.0884 (mmm) cc_final: -0.0215 (mmm) REVERT: E 311 LEU cc_start: 0.5438 (mt) cc_final: 0.4777 (mt) outliers start: 32 outliers final: 21 residues processed: 214 average time/residue: 0.1089 time to fit residues: 36.6618 Evaluate side-chains 197 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 115 ASN ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN E 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.224373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.194587 restraints weight = 37343.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.201469 restraints weight = 16946.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204177 restraints weight = 9861.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.206778 restraints weight = 7078.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.207921 restraints weight = 5343.573| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4346 r_free = 0.4346 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4346 r_free = 0.4346 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 1.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 14098 Z= 0.228 Angle : 0.852 14.029 19190 Z= 0.428 Chirality : 0.052 0.455 2185 Planarity : 0.006 0.079 2395 Dihedral : 6.668 58.810 1954 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.82 % Favored : 93.88 % Rotamer: Outliers : 2.28 % Allowed : 18.77 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1686 helix: 1.40 (0.22), residues: 579 sheet: -1.45 (0.26), residues: 376 loop : -1.42 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 119 TYR 0.020 0.002 TYR D 161 PHE 0.036 0.003 PHE D 207 TRP 0.030 0.003 TRP A 415 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00505 (14083) covalent geometry : angle 0.84491 (19155) SS BOND : bond 0.01544 ( 10) SS BOND : angle 2.01377 ( 20) hydrogen bonds : bond 0.03555 ( 512) hydrogen bonds : angle 4.88009 ( 1449) link_NAG-ASN : bond 0.00801 ( 5) link_NAG-ASN : angle 3.47715 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4770 (mpp) cc_final: 0.2552 (tmm) REVERT: A 51 ILE cc_start: 0.7702 (mp) cc_final: 0.7453 (mt) REVERT: A 136 LEU cc_start: 0.7951 (mt) cc_final: 0.7617 (tp) REVERT: A 163 MET cc_start: 0.0271 (mtt) cc_final: -0.2120 (tpt) REVERT: A 246 MET cc_start: 0.5731 (tmm) cc_final: 0.5492 (tmm) REVERT: A 263 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.4305 (tpp) REVERT: A 273 SER cc_start: 0.7979 (t) cc_final: 0.7711 (p) REVERT: B 163 MET cc_start: 0.3834 (ppp) cc_final: 0.2495 (mtp) REVERT: B 246 MET cc_start: 0.4527 (pmm) cc_final: 0.3105 (ptp) REVERT: B 263 MET cc_start: 0.4395 (ppp) cc_final: 0.2427 (ppp) REVERT: B 417 ILE cc_start: 0.7589 (tt) cc_final: 0.7282 (tt) REVERT: D 111 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6065 (m) REVERT: D 164 ASN cc_start: 0.5835 (t0) cc_final: 0.5555 (t0) REVERT: D 246 MET cc_start: 0.4470 (mmt) cc_final: 0.4214 (tpt) REVERT: E 177 MET cc_start: 0.1590 (mmm) cc_final: -0.0154 (mmm) REVERT: E 277 VAL cc_start: 0.1801 (OUTLIER) cc_final: 0.1546 (t) outliers start: 34 outliers final: 22 residues processed: 265 average time/residue: 0.0948 time to fit residues: 39.9469 Evaluate side-chains 241 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 36 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 chunk 160 optimal weight: 0.0270 chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 177 GLN C 186 GLN D 66 GLN D 109 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.224587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.194710 restraints weight = 49735.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.202556 restraints weight = 20906.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.205630 restraints weight = 9795.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.206617 restraints weight = 6469.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.207827 restraints weight = 6008.281| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4377 r_free = 0.4377 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4377 r_free = 0.4377 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 1.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14098 Z= 0.127 Angle : 0.719 14.161 19190 Z= 0.344 Chirality : 0.045 0.209 2185 Planarity : 0.004 0.050 2395 Dihedral : 6.314 59.736 1954 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 20.31 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1686 helix: 1.76 (0.23), residues: 565 sheet: -1.32 (0.26), residues: 386 loop : -1.27 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 65 TYR 0.021 0.001 TYR E 224 PHE 0.032 0.002 PHE A 295 TRP 0.022 0.001 TRP E 263 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00276 (14083) covalent geometry : angle 0.71146 (19155) SS BOND : bond 0.00250 ( 10) SS BOND : angle 1.64821 ( 20) hydrogen bonds : bond 0.03028 ( 512) hydrogen bonds : angle 4.61150 ( 1449) link_NAG-ASN : bond 0.00623 ( 5) link_NAG-ASN : angle 3.28434 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4453 (mpp) cc_final: 0.2746 (ttp) REVERT: A 163 MET cc_start: -0.0122 (mtt) cc_final: -0.2101 (tpt) REVERT: A 227 MET cc_start: 0.5749 (tpp) cc_final: 0.5229 (tpp) REVERT: A 263 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.4630 (ttt) REVERT: B 163 MET cc_start: 0.3906 (ppp) cc_final: 0.2995 (mtp) REVERT: B 225 ILE cc_start: 0.8406 (mt) cc_final: 0.8157 (mm) REVERT: B 263 MET cc_start: 0.4317 (ppp) cc_final: 0.2616 (ppp) REVERT: C 147 MET cc_start: 0.6629 (mpp) cc_final: 0.6057 (mtt) REVERT: C 228 TYR cc_start: 0.7380 (m-10) cc_final: 0.7173 (m-10) REVERT: C 263 MET cc_start: 0.6651 (mmm) cc_final: 0.6388 (mmp) REVERT: D 100 PHE cc_start: 0.2667 (m-10) cc_final: 0.2186 (m-10) REVERT: D 239 TRP cc_start: 0.7462 (m-10) cc_final: 0.6008 (m100) REVERT: E 177 MET cc_start: 0.1724 (mmm) cc_final: 0.0288 (mmt) REVERT: E 277 VAL cc_start: 0.2384 (OUTLIER) cc_final: 0.2003 (t) REVERT: E 329 GLN cc_start: 0.3742 (mt0) cc_final: 0.3527 (mt0) outliers start: 28 outliers final: 20 residues processed: 239 average time/residue: 0.0860 time to fit residues: 33.2934 Evaluate side-chains 224 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 115 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.221751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.191550 restraints weight = 39179.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.198813 restraints weight = 16830.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.201148 restraints weight = 8833.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.201534 restraints weight = 6893.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.202690 restraints weight = 6078.837| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 1.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14098 Z= 0.147 Angle : 0.746 13.912 19190 Z= 0.364 Chirality : 0.046 0.241 2185 Planarity : 0.005 0.044 2395 Dihedral : 6.283 58.432 1954 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.46 % Favored : 95.31 % Rotamer: Outliers : 1.94 % Allowed : 21.11 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.21), residues: 1686 helix: 1.80 (0.23), residues: 566 sheet: -1.45 (0.26), residues: 397 loop : -1.19 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 271 TYR 0.033 0.001 TYR D 161 PHE 0.030 0.002 PHE A 295 TRP 0.018 0.002 TRP E 263 HIS 0.047 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00316 (14083) covalent geometry : angle 0.73836 (19155) SS BOND : bond 0.00258 ( 10) SS BOND : angle 1.76958 ( 20) hydrogen bonds : bond 0.02980 ( 512) hydrogen bonds : angle 4.58278 ( 1449) link_NAG-ASN : bond 0.00715 ( 5) link_NAG-ASN : angle 3.40218 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.07 seconds wall clock time: 42 minutes 47.90 seconds (2567.90 seconds total)