Starting phenix.real_space_refine on Sun Aug 24 03:57:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frw_29409/08_2025/8frw_29409.map" } resolution = 2.92 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= 0.000 sd= 0.003 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 50 5.16 5 C 10990 2.51 5 N 2705 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16680 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, D, E Time building chain proxies: 4.00, per 1000 atoms: 0.24 Number of scatterers: 16680 At special positions: 0 Unit cell: (95.7, 96.8, 171.6, 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 50 16.00 O 2935 8.00 N 2705 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 687.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 43.5% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.682A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 220 through 243 removed outlier: 4.001A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.683A pdb=" N LEU A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 220 through 243 removed outlier: 4.002A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 250 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 462 removed outlier: 3.694A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 220 through 243 removed outlier: 4.001A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 250 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.682A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.002A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.869A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 220 through 243 removed outlier: 4.003A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 250 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 462 removed outlier: 3.694A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.313A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.313A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLU A 71 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N THR A 38 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.495A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 71 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR B 38 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 71 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N THR C 38 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU D 71 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR D 38 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU E 71 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR E 38 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.495A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2610 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: 2.61 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2550 1.32 - 1.44: 4900 1.44 - 1.57: 9620 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17145 Sorted by residual: bond pdb=" C16 Y7H A 504 " pdb=" C17 Y7H A 504 " ideal model delta sigma weight residual 1.559 1.492 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C16 Y7H B 501 " pdb=" C17 Y7H B 501 " ideal model delta sigma weight residual 1.559 1.492 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C16 Y7H E 501 " pdb=" C17 Y7H E 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C16 Y7H D 501 " pdb=" C17 Y7H D 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C16 Y7H C 501 " pdb=" C17 Y7H C 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 17140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 22777 2.03 - 4.07: 521 4.07 - 6.10: 102 6.10 - 8.13: 25 8.13 - 10.17: 15 Bond angle restraints: 23440 Sorted by residual: angle pdb=" N ILE C 203 " pdb=" CA ILE C 203 " pdb=" C ILE C 203 " ideal model delta sigma weight residual 112.80 104.12 8.68 1.15e+00 7.56e-01 5.69e+01 angle pdb=" N ILE D 203 " pdb=" CA ILE D 203 " pdb=" C ILE D 203 " ideal model delta sigma weight residual 112.80 104.14 8.66 1.15e+00 7.56e-01 5.67e+01 angle pdb=" N ILE B 203 " pdb=" CA ILE B 203 " pdb=" C ILE B 203 " ideal model delta sigma weight residual 112.80 104.15 8.65 1.15e+00 7.56e-01 5.66e+01 angle pdb=" N ILE E 203 " pdb=" CA ILE E 203 " pdb=" C ILE E 203 " ideal model delta sigma weight residual 112.80 104.18 8.62 1.15e+00 7.56e-01 5.61e+01 angle pdb=" N ILE A 203 " pdb=" CA ILE A 203 " pdb=" C ILE A 203 " ideal model delta sigma weight residual 112.80 104.19 8.61 1.15e+00 7.56e-01 5.61e+01 ... (remaining 23435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 9364 17.49 - 34.97: 837 34.97 - 52.46: 154 52.46 - 69.95: 20 69.95 - 87.43: 5 Dihedral angle restraints: 10380 sinusoidal: 4485 harmonic: 5895 Sorted by residual: dihedral pdb=" CA ILE B 163 " pdb=" C ILE B 163 " pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ILE D 163 " pdb=" C ILE D 163 " pdb=" N ASN D 164 " pdb=" CA ASN D 164 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE A 163 " pdb=" C ILE A 163 " pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 10377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1884 0.039 - 0.077: 569 0.077 - 0.116: 216 0.116 - 0.155: 68 0.155 - 0.193: 18 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 2752 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 44 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C ILE A 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 44 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE C 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET C 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE B 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE B 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET B 45 " -0.017 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4678 2.83 - 3.35: 15365 3.35 - 3.86: 27578 3.86 - 4.38: 29713 4.38 - 4.90: 52128 Nonbonded interactions: 129462 Sorted by model distance: nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.312 3.040 ... (remaining 129457 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 462 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.090 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.067 17165 Z= 0.239 Angle : 0.792 10.168 23495 Z= 0.413 Chirality : 0.048 0.193 2755 Planarity : 0.005 0.038 2840 Dihedral : 13.230 87.432 6525 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.11 % Allowed : 0.98 % Favored : 98.92 % 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: 0.72 (0.19), residues: 1955 helix: 2.24 (0.19), residues: 735 sheet: -0.03 (0.26), residues: 355 loop : -0.86 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 424 TYR 0.016 0.001 TYR B 67 PHE 0.017 0.002 PHE B 233 TRP 0.041 0.002 TRP D 320 HIS 0.003 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00464 (17145) covalent geometry : angle 0.76744 (23440) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.51733 ( 10) hydrogen bonds : bond 0.11774 ( 840) hydrogen bonds : angle 4.95822 ( 2610) link_NAG-ASN : bond 0.00322 ( 15) link_NAG-ASN : angle 4.55208 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.651 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.4797 time to fit residues: 87.4448 Evaluate side-chains 65 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056621 restraints weight = 42224.384| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.82 r_work: 0.2745 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17165 Z= 0.217 Angle : 0.657 7.556 23495 Z= 0.323 Chirality : 0.045 0.154 2755 Planarity : 0.004 0.033 2840 Dihedral : 5.344 31.332 2645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.46 % Allowed : 8.29 % Favored : 90.24 % 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: 0.89 (0.20), residues: 1955 helix: 2.36 (0.19), residues: 765 sheet: -0.08 (0.27), residues: 330 loop : -0.78 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 169 TYR 0.027 0.002 TYR C 116 PHE 0.009 0.001 PHE E 303 TRP 0.016 0.002 TRP B 320 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00524 (17145) covalent geometry : angle 0.63871 (23440) SS BOND : bond 0.00606 ( 5) SS BOND : angle 0.96987 ( 10) hydrogen bonds : bond 0.05209 ( 840) hydrogen bonds : angle 4.23015 ( 2610) link_NAG-ASN : bond 0.00411 ( 15) link_NAG-ASN : angle 3.57506 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.573 Fit side-chains REVERT: A 235 MET cc_start: 0.8561 (mmp) cc_final: 0.8068 (mpp) REVERT: A 267 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 242 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8364 (t80) REVERT: D 267 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8657 (tp) REVERT: E 54 LYS cc_start: 0.8958 (pttm) cc_final: 0.8749 (pmtt) REVERT: E 267 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8664 (tp) outliers start: 27 outliers final: 3 residues processed: 103 average time/residue: 0.3998 time to fit residues: 48.0784 Evaluate side-chains 67 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 138 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.054854 restraints weight = 41915.688| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.81 r_work: 0.2689 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17165 Z= 0.206 Angle : 0.631 7.034 23495 Z= 0.309 Chirality : 0.045 0.157 2755 Planarity : 0.004 0.032 2840 Dihedral : 5.136 25.174 2645 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.41 % Allowed : 10.79 % Favored : 87.80 % 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: 1.01 (0.20), residues: 1955 helix: 2.50 (0.19), residues: 795 sheet: -0.11 (0.26), residues: 330 loop : -0.83 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 315 TYR 0.025 0.002 TYR A 116 PHE 0.013 0.001 PHE C 254 TRP 0.017 0.002 TRP D 320 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00491 (17145) covalent geometry : angle 0.60881 (23440) SS BOND : bond 0.00610 ( 5) SS BOND : angle 0.92045 ( 10) hydrogen bonds : bond 0.05810 ( 840) hydrogen bonds : angle 4.20667 ( 2610) link_NAG-ASN : bond 0.00228 ( 15) link_NAG-ASN : angle 3.81371 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.468 Fit side-chains REVERT: A 267 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8563 (tp) REVERT: B 267 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8596 (tp) REVERT: C 267 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 267 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8683 (tp) REVERT: E 235 MET cc_start: 0.8755 (mmm) cc_final: 0.8491 (mmm) REVERT: E 267 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8579 (tp) outliers start: 26 outliers final: 11 residues processed: 102 average time/residue: 0.4194 time to fit residues: 49.4970 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.055389 restraints weight = 41636.031| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.76 r_work: 0.2708 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17165 Z= 0.139 Angle : 0.571 9.236 23495 Z= 0.276 Chirality : 0.043 0.130 2755 Planarity : 0.003 0.031 2840 Dihedral : 4.783 26.226 2645 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.01 % Allowed : 11.17 % Favored : 86.83 % 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: 1.10 (0.20), residues: 1955 helix: 2.60 (0.19), residues: 795 sheet: -0.16 (0.25), residues: 330 loop : -0.78 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.015 0.001 TYR C 67 PHE 0.010 0.001 PHE B 242 TRP 0.016 0.001 TRP A 320 HIS 0.002 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00317 (17145) covalent geometry : angle 0.55395 (23440) SS BOND : bond 0.00426 ( 5) SS BOND : angle 0.79439 ( 10) hydrogen bonds : bond 0.05289 ( 840) hydrogen bonds : angle 4.05637 ( 2610) link_NAG-ASN : bond 0.00227 ( 15) link_NAG-ASN : angle 3.15909 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.652 Fit side-chains REVERT: A 235 MET cc_start: 0.8595 (tpp) cc_final: 0.8004 (mpp) REVERT: A 267 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8527 (tp) REVERT: B 267 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8649 (tp) REVERT: C 235 MET cc_start: 0.8912 (tpp) cc_final: 0.8243 (mpp) REVERT: C 267 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8580 (tp) REVERT: D 267 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (tp) REVERT: E 267 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8490 (tp) outliers start: 37 outliers final: 10 residues processed: 103 average time/residue: 0.3806 time to fit residues: 46.4420 Evaluate side-chains 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 172 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053280 restraints weight = 41839.034| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.74 r_work: 0.2664 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17165 Z= 0.214 Angle : 0.644 10.119 23495 Z= 0.310 Chirality : 0.046 0.143 2755 Planarity : 0.004 0.032 2840 Dihedral : 5.200 28.688 2645 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.38 % Allowed : 12.74 % Favored : 84.88 % 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: 1.00 (0.20), residues: 1955 helix: 2.60 (0.19), residues: 795 sheet: -0.20 (0.25), residues: 330 loop : -0.92 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.022 0.002 TYR C 67 PHE 0.010 0.001 PHE C 103 TRP 0.019 0.002 TRP D 320 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00513 (17145) covalent geometry : angle 0.61982 (23440) SS BOND : bond 0.00610 ( 5) SS BOND : angle 1.10109 ( 10) hydrogen bonds : bond 0.06058 ( 840) hydrogen bonds : angle 4.25244 ( 2610) link_NAG-ASN : bond 0.00243 ( 15) link_NAG-ASN : angle 4.03336 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 0.681 Fit side-chains REVERT: A 267 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8590 (tp) REVERT: B 267 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8619 (tp) REVERT: C 91 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8747 (p0) REVERT: C 235 MET cc_start: 0.8912 (tpp) cc_final: 0.8079 (mpp) REVERT: C 267 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8579 (tp) REVERT: D 267 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (tp) REVERT: E 267 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8558 (tp) outliers start: 44 outliers final: 21 residues processed: 105 average time/residue: 0.3530 time to fit residues: 43.9474 Evaluate side-chains 85 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 0.0030 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.080916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054268 restraints weight = 41487.473| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.76 r_work: 0.2683 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17165 Z= 0.150 Angle : 0.588 10.258 23495 Z= 0.282 Chirality : 0.043 0.130 2755 Planarity : 0.003 0.032 2840 Dihedral : 4.903 28.811 2645 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.33 % Allowed : 13.17 % Favored : 84.50 % 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: 1.03 (0.20), residues: 1955 helix: 2.69 (0.19), residues: 795 sheet: -0.26 (0.25), residues: 330 loop : -0.94 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 315 TYR 0.015 0.001 TYR C 67 PHE 0.008 0.001 PHE A 242 TRP 0.020 0.001 TRP A 320 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00346 (17145) covalent geometry : angle 0.56752 (23440) SS BOND : bond 0.00464 ( 5) SS BOND : angle 0.90920 ( 10) hydrogen bonds : bond 0.05599 ( 840) hydrogen bonds : angle 4.10915 ( 2610) link_NAG-ASN : bond 0.00190 ( 15) link_NAG-ASN : angle 3.51353 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.655 Fit side-chains REVERT: A 267 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 267 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8606 (tp) REVERT: C 235 MET cc_start: 0.8854 (tpp) cc_final: 0.8042 (mpp) REVERT: C 267 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 57 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8424 (p) REVERT: D 267 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (tp) REVERT: E 91 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8739 (p0) REVERT: E 267 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8504 (tp) outliers start: 43 outliers final: 27 residues processed: 108 average time/residue: 0.3653 time to fit residues: 47.1376 Evaluate side-chains 95 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 454 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 117 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055051 restraints weight = 41150.102| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.75 r_work: 0.2701 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17165 Z= 0.121 Angle : 0.555 9.858 23495 Z= 0.268 Chirality : 0.043 0.138 2755 Planarity : 0.003 0.031 2840 Dihedral : 4.709 29.205 2645 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 13.01 % Favored : 84.34 % 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: 1.08 (0.20), residues: 1955 helix: 2.71 (0.19), residues: 795 sheet: -0.26 (0.26), residues: 330 loop : -0.89 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 315 TYR 0.012 0.001 TYR C 67 PHE 0.009 0.001 PHE D 233 TRP 0.028 0.001 TRP E 320 HIS 0.002 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00262 (17145) covalent geometry : angle 0.53912 (23440) SS BOND : bond 0.00351 ( 5) SS BOND : angle 0.79616 ( 10) hydrogen bonds : bond 0.05259 ( 840) hydrogen bonds : angle 3.97671 ( 2610) link_NAG-ASN : bond 0.00252 ( 15) link_NAG-ASN : angle 3.09013 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 64 time to evaluate : 0.670 Fit side-chains REVERT: A 57 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8457 (p) REVERT: A 267 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (tp) REVERT: B 267 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 57 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 235 MET cc_start: 0.8870 (tpp) cc_final: 0.8126 (mpp) REVERT: C 267 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 267 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8642 (tp) REVERT: E 91 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8731 (p0) REVERT: E 235 MET cc_start: 0.8812 (tpp) cc_final: 0.8547 (mmm) REVERT: E 267 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (tp) outliers start: 49 outliers final: 29 residues processed: 110 average time/residue: 0.3828 time to fit residues: 50.3255 Evaluate side-chains 99 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 454 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.080074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053432 restraints weight = 41542.462| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.74 r_work: 0.2667 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17165 Z= 0.190 Angle : 0.625 9.852 23495 Z= 0.299 Chirality : 0.045 0.139 2755 Planarity : 0.004 0.032 2840 Dihedral : 5.026 29.851 2645 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.82 % Allowed : 13.22 % Favored : 83.96 % 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: 0.99 (0.20), residues: 1955 helix: 2.67 (0.19), residues: 795 sheet: -0.28 (0.26), residues: 330 loop : -0.99 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 315 TYR 0.021 0.001 TYR B 67 PHE 0.009 0.001 PHE D 233 TRP 0.026 0.002 TRP E 320 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00451 (17145) covalent geometry : angle 0.60180 (23440) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.06454 ( 10) hydrogen bonds : bond 0.05807 ( 840) hydrogen bonds : angle 4.13591 ( 2610) link_NAG-ASN : bond 0.00207 ( 15) link_NAG-ASN : angle 3.84318 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 67 time to evaluate : 0.614 Fit side-chains REVERT: A 57 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 267 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8500 (tp) REVERT: B 267 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8617 (tp) REVERT: C 57 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 235 MET cc_start: 0.8894 (tpp) cc_final: 0.8022 (mpp) REVERT: C 267 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (tp) REVERT: D 57 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8465 (p) REVERT: D 267 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8707 (tp) REVERT: E 91 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8972 (p0) REVERT: E 235 MET cc_start: 0.8889 (tpp) cc_final: 0.8067 (mpp) REVERT: E 267 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8602 (tp) outliers start: 52 outliers final: 32 residues processed: 117 average time/residue: 0.3647 time to fit residues: 51.0859 Evaluate side-chains 103 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 454 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 18 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054582 restraints weight = 41299.074| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.75 r_work: 0.2690 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17165 Z= 0.130 Angle : 0.574 10.198 23495 Z= 0.275 Chirality : 0.043 0.149 2755 Planarity : 0.003 0.034 2840 Dihedral : 4.797 29.515 2645 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.38 % Allowed : 13.93 % Favored : 83.69 % 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: 1.05 (0.20), residues: 1955 helix: 2.72 (0.19), residues: 795 sheet: -0.29 (0.26), residues: 330 loop : -0.95 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 315 TYR 0.013 0.001 TYR B 67 PHE 0.011 0.001 PHE E 233 TRP 0.038 0.002 TRP B 320 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00289 (17145) covalent geometry : angle 0.55515 (23440) SS BOND : bond 0.00374 ( 5) SS BOND : angle 0.83498 ( 10) hydrogen bonds : bond 0.05378 ( 840) hydrogen bonds : angle 4.00087 ( 2610) link_NAG-ASN : bond 0.00244 ( 15) link_NAG-ASN : angle 3.34989 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.642 Fit side-chains REVERT: A 57 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 267 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 267 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 57 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 267 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8591 (tp) REVERT: D 57 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8360 (p) REVERT: D 267 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8656 (tp) REVERT: E 91 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8718 (p0) REVERT: E 235 MET cc_start: 0.8857 (tpp) cc_final: 0.8490 (mmm) REVERT: E 267 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8566 (tp) outliers start: 44 outliers final: 31 residues processed: 107 average time/residue: 0.3443 time to fit residues: 44.9658 Evaluate side-chains 99 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.082471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.055894 restraints weight = 41057.616| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.75 r_work: 0.2721 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17165 Z= 0.109 Angle : 0.557 11.597 23495 Z= 0.267 Chirality : 0.042 0.156 2755 Planarity : 0.003 0.040 2840 Dihedral : 4.567 29.857 2645 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.33 % Allowed : 13.98 % Favored : 83.69 % 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: 1.11 (0.20), residues: 1955 helix: 2.73 (0.19), residues: 795 sheet: -0.23 (0.26), residues: 330 loop : -0.88 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 315 TYR 0.012 0.001 TYR D 262 PHE 0.014 0.001 PHE B 233 TRP 0.050 0.002 TRP B 320 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00226 (17145) covalent geometry : angle 0.54392 (23440) SS BOND : bond 0.00281 ( 5) SS BOND : angle 0.74733 ( 10) hydrogen bonds : bond 0.04881 ( 840) hydrogen bonds : angle 3.86127 ( 2610) link_NAG-ASN : bond 0.00266 ( 15) link_NAG-ASN : angle 2.80873 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.664 Fit side-chains REVERT: A 267 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 267 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 57 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8392 (p) REVERT: C 267 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8532 (tp) REVERT: D 267 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8594 (tp) REVERT: E 182 ILE cc_start: 0.7183 (mm) cc_final: 0.6815 (mt) REVERT: E 235 MET cc_start: 0.8795 (tpp) cc_final: 0.8531 (mmm) REVERT: E 267 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8566 (tp) outliers start: 43 outliers final: 27 residues processed: 111 average time/residue: 0.3175 time to fit residues: 43.2069 Evaluate side-chains 93 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 126 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.082172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055513 restraints weight = 41159.555| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.75 r_work: 0.2715 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17165 Z= 0.114 Angle : 0.564 10.440 23495 Z= 0.270 Chirality : 0.042 0.154 2755 Planarity : 0.004 0.039 2840 Dihedral : 4.572 30.094 2645 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 14.58 % Favored : 83.36 % 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: 1.10 (0.20), residues: 1955 helix: 2.69 (0.19), residues: 795 sheet: -0.21 (0.26), residues: 330 loop : -0.86 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 315 TYR 0.012 0.001 TYR C 67 PHE 0.020 0.001 PHE D 233 TRP 0.053 0.002 TRP D 320 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00247 (17145) covalent geometry : angle 0.54970 (23440) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.78647 ( 10) hydrogen bonds : bond 0.04866 ( 840) hydrogen bonds : angle 3.86197 ( 2610) link_NAG-ASN : bond 0.00256 ( 15) link_NAG-ASN : angle 2.87831 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.05 seconds wall clock time: 70 minutes 6.35 seconds (4206.35 seconds total)