Starting phenix.real_space_refine on Mon Nov 18 15:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_29409.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_29409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_29409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_29409.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/11_2024/8frw_29409.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 8.84, per 1000 atoms: 0.53 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=2, 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 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: 4.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.63 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: 4.93 Time building geometry restraints manager: 4.84 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: 828 34.97 - 52.46: 154 52.46 - 69.95: 20 69.95 - 87.43: 5 Dihedral angle restraints: 10371 sinusoidal: 4476 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 10368 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: 2.03 - 2.61: 93 2.61 - 3.18: 13534 3.18 - 3.75: 25542 3.75 - 4.33: 34019 4.33 - 4.90: 56283 Nonbonded interactions: 129471 Sorted by model distance: nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.033 3.760 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 ... (remaining 129466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 35.770 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.440 ------------------------------------------------------------------------------- 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 17145 Z= 0.299 Angle : 0.767 10.168 23440 Z= 0.408 Chirality : 0.048 0.193 2755 Planarity : 0.005 0.038 2840 Dihedral : 13.230 87.432 6525 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.041 0.002 TRP D 320 HIS 0.003 0.001 HIS E 323 PHE 0.017 0.002 PHE B 233 TYR 0.016 0.001 TYR B 67 ARG 0.007 0.000 ARG D 424 *********************** 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 : 1.925 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 1.0538 time to fit residues: 193.8406 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 : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0070 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17145 Z= 0.164 Angle : 0.543 7.130 23440 Z= 0.272 Chirality : 0.042 0.136 2755 Planarity : 0.004 0.035 2840 Dihedral : 5.132 34.678 2645 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.25 % Allowed : 7.26 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1955 helix: 2.28 (0.19), residues: 770 sheet: 0.00 (0.28), residues: 330 loop : -0.69 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 459 HIS 0.003 0.000 HIS A 323 PHE 0.005 0.001 PHE A 254 TYR 0.014 0.001 TYR E 116 ARG 0.003 0.000 ARG A 424 *********************** 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 101 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 267 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 242 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8352 (t80) REVERT: D 267 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8591 (tp) REVERT: E 267 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8508 (tp) outliers start: 23 outliers final: 10 residues processed: 97 average time/residue: 0.9760 time to fit residues: 111.6558 Evaluate side-chains 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 233 PHE 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 295 VAL Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17145 Z= 0.259 Angle : 0.596 7.684 23440 Z= 0.298 Chirality : 0.045 0.150 2755 Planarity : 0.004 0.034 2840 Dihedral : 5.031 24.177 2645 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.41 % Allowed : 9.92 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1955 helix: 2.37 (0.19), residues: 795 sheet: -0.06 (0.27), residues: 330 loop : -0.74 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 320 HIS 0.004 0.001 HIS C 119 PHE 0.010 0.001 PHE A 242 TYR 0.028 0.002 TYR A 116 ARG 0.013 0.000 ARG E 315 *********************** 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 : 2.038 Fit side-chains REVERT: A 267 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8530 (tp) REVERT: B 267 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8626 (tp) REVERT: C 267 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8489 (tp) REVERT: D 267 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8673 (tp) REVERT: E 235 MET cc_start: 0.8792 (mmm) cc_final: 0.8462 (mmm) REVERT: E 267 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8557 (tp) outliers start: 26 outliers final: 5 residues processed: 100 average time/residue: 1.0164 time to fit residues: 118.3805 Evaluate side-chains 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 450 ILE 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 E residue 267 ILE Chi-restraints excluded: chain E residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 188 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17145 Z= 0.137 Angle : 0.515 9.348 23440 Z= 0.253 Chirality : 0.042 0.127 2755 Planarity : 0.003 0.031 2840 Dihedral : 4.437 24.150 2645 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.41 % Allowed : 10.95 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1955 helix: 2.67 (0.20), residues: 765 sheet: -0.03 (0.26), residues: 330 loop : -0.54 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 320 HIS 0.001 0.000 HIS E 18 PHE 0.011 0.001 PHE C 242 TYR 0.011 0.001 TYR C 67 ARG 0.004 0.000 ARG E 315 *********************** 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 107 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 2.135 Fit side-chains REVERT: A 182 ILE cc_start: 0.7199 (mm) cc_final: 0.6794 (mt) REVERT: A 267 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 182 ILE cc_start: 0.6677 (mm) cc_final: 0.6388 (mt) REVERT: B 267 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 419 MET cc_start: 0.8310 (mmp) cc_final: 0.8109 (mmp) REVERT: C 267 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8476 (tp) REVERT: D 267 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8586 (tp) REVERT: E 182 ILE cc_start: 0.7010 (mm) cc_final: 0.6715 (mt) REVERT: E 235 MET cc_start: 0.8762 (mmm) cc_final: 0.8422 (mmm) REVERT: E 267 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8479 (tp) outliers start: 26 outliers final: 5 residues processed: 104 average time/residue: 0.9085 time to fit residues: 111.4774 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 160 optimal weight: 0.0470 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17145 Z= 0.182 Angle : 0.530 10.053 23440 Z= 0.261 Chirality : 0.042 0.130 2755 Planarity : 0.003 0.033 2840 Dihedral : 4.503 25.579 2645 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.30 % Allowed : 12.36 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1955 helix: 2.56 (0.19), residues: 795 sheet: 0.01 (0.26), residues: 330 loop : -0.71 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 320 HIS 0.003 0.001 HIS E 323 PHE 0.007 0.001 PHE A 242 TYR 0.016 0.001 TYR C 67 ARG 0.006 0.000 ARG D 315 *********************** 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 97 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 1.956 Fit side-chains REVERT: A 267 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 182 ILE cc_start: 0.6773 (mm) cc_final: 0.6466 (mt) REVERT: B 267 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 291 MET cc_start: 0.8576 (mmm) cc_final: 0.8339 (mmm) REVERT: C 267 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8512 (tp) REVERT: D 267 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8648 (tp) REVERT: E 182 ILE cc_start: 0.7135 (mm) cc_final: 0.6783 (mt) REVERT: E 267 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8487 (tp) outliers start: 24 outliers final: 8 residues processed: 94 average time/residue: 0.9168 time to fit residues: 102.2810 Evaluate side-chains 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 308 VAL 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 202 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 188 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17145 Z= 0.138 Angle : 0.515 10.277 23440 Z= 0.251 Chirality : 0.041 0.126 2755 Planarity : 0.003 0.031 2840 Dihedral : 4.323 25.342 2645 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.08 % Allowed : 13.28 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1955 helix: 2.65 (0.19), residues: 800 sheet: 0.02 (0.26), residues: 330 loop : -0.71 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 320 HIS 0.002 0.000 HIS E 323 PHE 0.007 0.001 PHE A 242 TYR 0.012 0.001 TYR C 67 ARG 0.006 0.000 ARG A 315 *********************** 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 94 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 1.971 Fit side-chains REVERT: A 267 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 182 ILE cc_start: 0.6767 (mm) cc_final: 0.6461 (mt) REVERT: B 267 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8624 (tp) REVERT: C 267 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8491 (tp) REVERT: D 182 ILE cc_start: 0.7000 (mm) cc_final: 0.6751 (mt) REVERT: D 267 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8572 (tp) REVERT: E 182 ILE cc_start: 0.7125 (mm) cc_final: 0.6775 (mt) REVERT: E 235 MET cc_start: 0.8791 (tpp) cc_final: 0.7972 (mpp) REVERT: E 267 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8479 (tp) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 0.9388 time to fit residues: 102.2662 Evaluate side-chains 82 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 308 VAL 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 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.0060 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17145 Z= 0.135 Angle : 0.510 10.321 23440 Z= 0.249 Chirality : 0.041 0.127 2755 Planarity : 0.003 0.032 2840 Dihedral : 4.242 25.362 2645 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.08 % Allowed : 13.55 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1955 helix: 2.66 (0.19), residues: 795 sheet: 0.07 (0.26), residues: 330 loop : -0.64 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 320 HIS 0.002 0.001 HIS E 323 PHE 0.007 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.007 0.000 ARG D 315 *********************** 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 97 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 2.102 Fit side-chains REVERT: A 267 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8365 (tp) REVERT: B 182 ILE cc_start: 0.6756 (mm) cc_final: 0.6451 (mt) REVERT: B 267 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8619 (tp) REVERT: C 267 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8497 (tp) REVERT: D 182 ILE cc_start: 0.6998 (mm) cc_final: 0.6751 (mt) REVERT: D 267 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8558 (tp) REVERT: E 182 ILE cc_start: 0.7124 (mm) cc_final: 0.6776 (mt) REVERT: E 267 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8456 (tp) outliers start: 20 outliers final: 8 residues processed: 96 average time/residue: 0.9386 time to fit residues: 106.5274 Evaluate side-chains 81 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 308 VAL 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 202 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17145 Z= 0.179 Angle : 0.541 11.179 23440 Z= 0.263 Chirality : 0.042 0.137 2755 Planarity : 0.003 0.042 2840 Dihedral : 4.407 26.376 2645 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 14.04 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1955 helix: 2.70 (0.19), residues: 800 sheet: 0.04 (0.26), residues: 330 loop : -0.68 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 320 HIS 0.002 0.001 HIS E 323 PHE 0.008 0.001 PHE D 233 TYR 0.016 0.001 TYR B 67 ARG 0.008 0.000 ARG E 315 *********************** 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 89 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 2.166 Fit side-chains REVERT: A 267 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8390 (tp) REVERT: B 182 ILE cc_start: 0.6821 (mm) cc_final: 0.6503 (mt) REVERT: B 235 MET cc_start: 0.8679 (tpp) cc_final: 0.8050 (mpp) REVERT: B 267 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8647 (tp) REVERT: C 235 MET cc_start: 0.8725 (tpp) cc_final: 0.8139 (mpp) REVERT: C 267 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8532 (tp) REVERT: D 182 ILE cc_start: 0.7046 (mm) cc_final: 0.6798 (mt) REVERT: D 267 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8592 (tp) REVERT: E 182 ILE cc_start: 0.7128 (mm) cc_final: 0.6774 (mt) REVERT: E 267 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8493 (tp) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.8951 time to fit residues: 93.8068 Evaluate side-chains 79 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 308 VAL 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 269 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 202 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 0.2980 chunk 105 optimal weight: 0.0770 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17145 Z= 0.140 Angle : 0.533 11.931 23440 Z= 0.257 Chirality : 0.042 0.143 2755 Planarity : 0.003 0.044 2840 Dihedral : 4.259 26.042 2645 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.92 % Allowed : 14.36 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1955 helix: 2.70 (0.19), residues: 800 sheet: 0.05 (0.26), residues: 330 loop : -0.65 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 320 HIS 0.002 0.000 HIS B 323 PHE 0.008 0.001 PHE D 233 TYR 0.011 0.001 TYR C 67 ARG 0.008 0.000 ARG B 315 *********************** 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 87 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 2.003 Fit side-chains REVERT: A 267 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8359 (tp) REVERT: B 182 ILE cc_start: 0.6880 (mm) cc_final: 0.6581 (mt) REVERT: B 235 MET cc_start: 0.8673 (tpp) cc_final: 0.8032 (mpp) REVERT: B 267 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8622 (tp) REVERT: C 235 MET cc_start: 0.8746 (tpp) cc_final: 0.8139 (mpp) REVERT: C 267 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8509 (tp) REVERT: D 182 ILE cc_start: 0.7031 (mm) cc_final: 0.6793 (mt) REVERT: D 267 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8564 (tp) REVERT: E 182 ILE cc_start: 0.7144 (mm) cc_final: 0.6790 (mt) REVERT: E 267 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8453 (tp) outliers start: 17 outliers final: 9 residues processed: 86 average time/residue: 0.8638 time to fit residues: 89.1131 Evaluate side-chains 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 308 VAL 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 269 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 87 optimal weight: 0.0050 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 0.0970 chunk 154 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17145 Z= 0.147 Angle : 0.534 12.060 23440 Z= 0.259 Chirality : 0.042 0.151 2755 Planarity : 0.004 0.048 2840 Dihedral : 4.269 26.723 2645 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.87 % Allowed : 14.58 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1955 helix: 2.70 (0.19), residues: 800 sheet: 0.07 (0.26), residues: 330 loop : -0.65 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 320 HIS 0.002 0.001 HIS D 323 PHE 0.007 0.001 PHE D 233 TYR 0.013 0.001 TYR C 67 ARG 0.010 0.000 ARG B 315 ********************** 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 82 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.895 Fit side-chains REVERT: A 267 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8359 (tp) REVERT: B 182 ILE cc_start: 0.6826 (mm) cc_final: 0.6531 (mt) REVERT: B 235 MET cc_start: 0.8720 (tpp) cc_final: 0.8101 (mpp) REVERT: B 267 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8628 (tp) REVERT: C 235 MET cc_start: 0.8751 (tpp) cc_final: 0.8118 (mpp) REVERT: C 267 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8509 (tp) REVERT: D 182 ILE cc_start: 0.7043 (mm) cc_final: 0.6797 (mt) REVERT: D 267 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8567 (tp) REVERT: E 182 ILE cc_start: 0.7114 (mm) cc_final: 0.6758 (mt) REVERT: E 267 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8447 (tp) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.9152 time to fit residues: 88.7178 Evaluate side-chains 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 308 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 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 27 VAL Chi-restraints excluded: chain D residue 202 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.083705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056946 restraints weight = 41533.950| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.76 r_work: 0.2751 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17145 Z= 0.149 Angle : 0.532 10.860 23440 Z= 0.259 Chirality : 0.042 0.150 2755 Planarity : 0.004 0.047 2840 Dihedral : 4.275 26.885 2645 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.03 % Allowed : 14.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1955 helix: 2.71 (0.19), residues: 800 sheet: 0.07 (0.26), residues: 330 loop : -0.64 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 320 HIS 0.002 0.001 HIS D 323 PHE 0.007 0.001 PHE B 233 TYR 0.013 0.001 TYR C 67 ARG 0.010 0.000 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3464.58 seconds wall clock time: 64 minutes 0.67 seconds (3840.67 seconds total)