Starting phenix.real_space_refine on Thu Feb 15 18:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cju_7484/02_2024/6cju_7484_updated.pdb" } resolution = 3.35 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= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8704 2.51 5 N 2080 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3102 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 24, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3102 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 24, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3102 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 24, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3102 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 24, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 7.22, per 1000 atoms: 0.55 Number of scatterers: 13076 At special positions: 0 Unit cell: (106.252, 106.252, 120.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2256 8.00 N 2080 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 55.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 Proline residue: A 31 - end of helix removed outlier: 3.760A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 4.324A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 105 through 125 removed outlier: 4.091A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 123 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.535A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.681A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 221 removed outlier: 3.811A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.862A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.637A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'B' and resid 13 through 35 Proline residue: B 31 - end of helix removed outlier: 3.760A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 removed outlier: 4.324A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 105 through 125 removed outlier: 4.091A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 125 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.535A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.681A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 221 removed outlier: 3.811A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.862A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.637A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'C' and resid 13 through 35 Proline residue: C 31 - end of helix removed outlier: 3.760A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 4.324A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 105 through 125 removed outlier: 4.091A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 115 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR C 123 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.535A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.681A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 221 removed outlier: 3.811A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.862A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.637A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'D' and resid 13 through 35 Proline residue: D 31 - end of helix removed outlier: 3.760A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 4.324A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 105 through 125 removed outlier: 4.091A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 115 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR D 123 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.535A pdb=" N ARG D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.681A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 221 removed outlier: 3.811A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.862A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 293 through 296 No H-bonds generated for 'chain 'D' and resid 293 through 296' Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.637A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 Processing helix chain 'D' and resid 405 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= B, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.717A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= D, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.717A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'C' and resid 380 through 383 removed outlier: 3.717A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= H, first strand: chain 'D' and resid 380 through 383 removed outlier: 3.717A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2444 1.33 - 1.44: 2976 1.44 - 1.56: 7856 1.56 - 1.68: 12 1.68 - 1.80: 52 Bond restraints: 13340 Sorted by residual: bond pdb=" O12 PGW B 501 " pdb=" P PGW B 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW C 501 " pdb=" P PGW C 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW D 501 " pdb=" P PGW D 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW A 501 " pdb=" P PGW A 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C03 PGW D 501 " pdb=" O11 PGW D 501 " ideal model delta sigma weight residual 1.412 1.363 0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 13335 not shown) Histogram of bond angle deviations from ideal: 98.80 - 106.26: 488 106.26 - 113.72: 7692 113.72 - 121.19: 6692 121.19 - 128.65: 3020 128.65 - 136.11: 120 Bond angle restraints: 18012 Sorted by residual: angle pdb=" C4' CMP A 500 " pdb=" C3' CMP A 500 " pdb=" O3' CMP A 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP B 500 " pdb=" C3' CMP B 500 " pdb=" O3' CMP B 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP D 500 " pdb=" C3' CMP D 500 " pdb=" O3' CMP D 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP C 500 " pdb=" C3' CMP C 500 " pdb=" O3' CMP C 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.88e+01 ... (remaining 18007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 7924 34.88 - 69.76: 180 69.76 - 104.64: 24 104.64 - 139.52: 24 139.52 - 174.39: 16 Dihedral angle restraints: 8168 sinusoidal: 3580 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP A 500 " pdb=" O3' CMP A 500 " pdb=" P CMP A 500 " pdb=" O1P CMP A 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP B 500 " pdb=" O3' CMP B 500 " pdb=" P CMP B 500 " pdb=" O1P CMP B 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP D 500 " pdb=" O3' CMP D 500 " pdb=" P CMP D 500 " pdb=" O1P CMP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1740 0.092 - 0.185: 324 0.185 - 0.277: 24 0.277 - 0.369: 4 0.369 - 0.461: 4 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 2093 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU C 93 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 93 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU B 93 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU B 93 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 93 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU D 93 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU D 93 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 94 " -0.021 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3312 2.80 - 3.33: 11396 3.33 - 3.85: 20876 3.85 - 4.38: 23088 4.38 - 4.90: 41884 Nonbonded interactions: 100556 Sorted by model distance: nonbonded pdb=" OH TYR B 175 " pdb=" OD2 ASP B 188 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR C 175 " pdb=" OD2 ASP C 188 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 175 " pdb=" OD2 ASP A 188 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR D 175 " pdb=" OD2 ASP D 188 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.322 2.440 ... (remaining 100551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.050 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: 4.420 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.230 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.011 0.079 13340 Z= 0.702 Angle : 1.501 10.258 18012 Z= 0.714 Chirality : 0.071 0.461 2096 Planarity : 0.009 0.058 2164 Dihedral : 18.925 174.394 5208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.49 % Allowed : 6.87 % Favored : 91.64 % 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: -4.12 (0.17), residues: 1544 helix: -2.63 (0.13), residues: 888 sheet: -1.79 (0.46), residues: 92 loop : -2.79 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 264 HIS 0.006 0.002 HIS B 292 PHE 0.014 0.003 PHE A 365 TYR 0.026 0.004 TYR A 211 ARG 0.005 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 1.423 Fit side-chains REVERT: B 171 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 233 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8013 (mtp85) REVERT: D 229 LYS cc_start: 0.9054 (tmtp) cc_final: 0.8847 (tttp) outliers start: 20 outliers final: 3 residues processed: 248 average time/residue: 0.3218 time to fit residues: 106.9442 Evaluate side-chains 121 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13340 Z= 0.194 Angle : 0.702 7.969 18012 Z= 0.330 Chirality : 0.042 0.202 2096 Planarity : 0.005 0.040 2164 Dihedral : 21.749 164.956 2268 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.36 % Allowed : 14.03 % Favored : 82.61 % 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: -1.98 (0.21), residues: 1544 helix: -0.68 (0.17), residues: 884 sheet: -1.19 (0.50), residues: 92 loop : -2.23 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 264 HIS 0.002 0.001 HIS C 281 PHE 0.009 0.001 PHE D 302 TYR 0.014 0.001 TYR B 128 ARG 0.004 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 1.431 Fit side-chains REVERT: A 126 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6900 (pp) REVERT: A 158 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8549 (pp) REVERT: A 233 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7837 (mtp85) REVERT: B 114 LYS cc_start: 0.8418 (tptp) cc_final: 0.8173 (tttp) REVERT: B 126 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6792 (pp) REVERT: B 158 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8554 (pp) REVERT: C 114 LYS cc_start: 0.8415 (tptp) cc_final: 0.8144 (tttp) REVERT: C 126 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6780 (pp) REVERT: C 158 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8537 (pp) REVERT: D 114 LYS cc_start: 0.8387 (tptp) cc_final: 0.7960 (tttp) REVERT: D 126 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6793 (pp) REVERT: D 158 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8545 (pp) outliers start: 45 outliers final: 12 residues processed: 198 average time/residue: 0.2484 time to fit residues: 71.6743 Evaluate side-chains 139 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13340 Z= 0.371 Angle : 0.753 9.236 18012 Z= 0.357 Chirality : 0.048 0.259 2096 Planarity : 0.005 0.046 2164 Dihedral : 20.067 164.367 2260 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.48 % Allowed : 15.90 % Favored : 79.63 % 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: -1.39 (0.22), residues: 1544 helix: -0.20 (0.18), residues: 904 sheet: -1.25 (0.50), residues: 88 loop : -1.97 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 176 HIS 0.003 0.001 HIS B 281 PHE 0.010 0.002 PHE C 309 TYR 0.016 0.002 TYR B 128 ARG 0.004 0.001 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 1.318 Fit side-chains REVERT: A 60 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7360 (tt) REVERT: A 126 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6949 (pp) REVERT: A 221 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 230 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 233 ARG cc_start: 0.8137 (ttt90) cc_final: 0.7882 (mtp85) REVERT: A 272 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: B 60 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7392 (tt) REVERT: B 126 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7076 (pp) REVERT: B 221 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8765 (tp) REVERT: B 230 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8478 (tp) REVERT: B 272 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: C 60 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7320 (tt) REVERT: C 126 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6975 (pp) REVERT: C 221 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 229 LYS cc_start: 0.9060 (tttt) cc_final: 0.8842 (tttp) REVERT: C 230 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8461 (tp) REVERT: C 272 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: D 60 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7315 (tt) REVERT: D 126 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6968 (pp) REVERT: D 221 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8773 (tp) REVERT: D 229 LYS cc_start: 0.9124 (tttt) cc_final: 0.8913 (tttp) REVERT: D 230 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8467 (tp) REVERT: D 272 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7681 (tp30) outliers start: 60 outliers final: 20 residues processed: 166 average time/residue: 0.2301 time to fit residues: 57.3250 Evaluate side-chains 146 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13340 Z= 0.186 Angle : 0.629 8.898 18012 Z= 0.292 Chirality : 0.043 0.263 2096 Planarity : 0.004 0.043 2164 Dihedral : 18.531 163.330 2260 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.63 % Allowed : 15.45 % Favored : 79.93 % 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: -0.77 (0.22), residues: 1544 helix: 0.29 (0.19), residues: 892 sheet: -1.00 (0.51), residues: 88 loop : -1.66 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 264 HIS 0.001 0.000 HIS A 232 PHE 0.006 0.001 PHE C 309 TYR 0.013 0.001 TYR A 128 ARG 0.002 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 123 time to evaluate : 1.320 Fit side-chains REVERT: A 60 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 114 LYS cc_start: 0.8243 (tptp) cc_final: 0.7823 (tttp) REVERT: A 126 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6852 (pp) REVERT: A 205 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 221 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8750 (tp) REVERT: A 230 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8536 (tp) REVERT: A 233 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7802 (mtp85) REVERT: A 272 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: B 60 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7287 (tt) REVERT: B 126 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6865 (pp) REVERT: B 205 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 221 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8728 (tp) REVERT: B 230 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 236 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 272 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7451 (tp30) REVERT: C 60 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7323 (tt) REVERT: C 126 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6847 (pp) REVERT: C 158 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8938 (pp) REVERT: C 205 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8766 (mm) REVERT: C 221 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8726 (tp) REVERT: C 229 LYS cc_start: 0.9045 (tttt) cc_final: 0.8804 (tttp) REVERT: C 230 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8529 (tp) REVERT: C 272 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: D 60 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7326 (tt) REVERT: D 114 LYS cc_start: 0.8230 (tptp) cc_final: 0.7855 (tttp) REVERT: D 126 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6894 (pp) REVERT: D 158 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8936 (pp) REVERT: D 205 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (mm) REVERT: D 221 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8729 (tp) REVERT: D 230 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8543 (tp) REVERT: D 272 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7451 (tp30) outliers start: 62 outliers final: 24 residues processed: 179 average time/residue: 0.2532 time to fit residues: 66.0924 Evaluate side-chains 167 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 116 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13340 Z= 0.275 Angle : 0.659 8.500 18012 Z= 0.308 Chirality : 0.045 0.283 2096 Planarity : 0.004 0.044 2164 Dihedral : 17.968 163.578 2260 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.37 % Allowed : 16.19 % Favored : 78.43 % 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: -0.69 (0.23), residues: 1544 helix: 0.26 (0.19), residues: 916 sheet: -0.90 (0.52), residues: 88 loop : -1.51 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 264 HIS 0.002 0.001 HIS B 281 PHE 0.008 0.001 PHE D 309 TYR 0.012 0.001 TYR A 175 ARG 0.003 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 112 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7376 (tt) REVERT: A 114 LYS cc_start: 0.8268 (tptp) cc_final: 0.7806 (tttp) REVERT: A 126 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6911 (pp) REVERT: A 205 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8719 (mm) REVERT: A 221 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 229 LYS cc_start: 0.9020 (tttp) cc_final: 0.8704 (tttt) REVERT: A 230 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 233 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7775 (mtp85) REVERT: A 272 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: A 389 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 60 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7394 (tt) REVERT: B 126 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6976 (pp) REVERT: B 205 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 221 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8736 (tp) REVERT: B 229 LYS cc_start: 0.9049 (tttp) cc_final: 0.8722 (tttt) REVERT: B 230 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8504 (tp) REVERT: B 236 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 272 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: B 389 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8568 (pp) REVERT: C 60 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7393 (tt) REVERT: C 126 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6982 (pp) REVERT: C 205 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 221 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8737 (tp) REVERT: C 229 LYS cc_start: 0.9081 (tttt) cc_final: 0.8862 (tttp) REVERT: C 230 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8486 (tp) REVERT: C 236 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 272 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: C 389 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8574 (pp) REVERT: D 60 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7267 (tt) REVERT: D 114 LYS cc_start: 0.8236 (tptp) cc_final: 0.7829 (tttp) REVERT: D 126 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7062 (pp) REVERT: D 205 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8714 (mm) REVERT: D 221 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8738 (tp) REVERT: D 230 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (tp) REVERT: D 236 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (p) REVERT: D 272 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: D 389 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8567 (pp) outliers start: 72 outliers final: 26 residues processed: 180 average time/residue: 0.2314 time to fit residues: 62.4925 Evaluate side-chains 165 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 108 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13340 Z= 0.168 Angle : 0.610 8.780 18012 Z= 0.281 Chirality : 0.042 0.269 2096 Planarity : 0.004 0.042 2164 Dihedral : 16.872 162.621 2260 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.63 % Allowed : 16.79 % Favored : 78.58 % 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: -0.31 (0.23), residues: 1544 helix: 0.65 (0.19), residues: 892 sheet: -0.88 (0.51), residues: 88 loop : -1.42 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 264 HIS 0.001 0.000 HIS D 232 PHE 0.006 0.001 PHE D 309 TYR 0.009 0.001 TYR A 128 ARG 0.002 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 127 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8847 (pp) REVERT: A 221 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8711 (tp) REVERT: A 229 LYS cc_start: 0.9002 (tttp) cc_final: 0.8666 (tttt) REVERT: A 230 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8550 (tp) REVERT: A 233 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7723 (mtp85) REVERT: A 272 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: B 158 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8851 (pp) REVERT: B 221 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8708 (tp) REVERT: B 229 LYS cc_start: 0.9009 (tttp) cc_final: 0.8695 (tttt) REVERT: B 230 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 272 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: C 60 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7270 (tt) REVERT: C 158 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8873 (pp) REVERT: C 221 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8710 (tp) REVERT: C 229 LYS cc_start: 0.9036 (tttt) cc_final: 0.8722 (tttp) REVERT: C 230 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8515 (tp) REVERT: C 236 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (p) REVERT: C 272 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: D 158 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8873 (pp) REVERT: D 221 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8710 (tp) REVERT: D 229 LYS cc_start: 0.8971 (tttp) cc_final: 0.8620 (tttt) REVERT: D 230 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 236 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8443 (p) REVERT: D 272 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7474 (tp30) outliers start: 62 outliers final: 19 residues processed: 184 average time/residue: 0.2305 time to fit residues: 63.6457 Evaluate side-chains 161 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13340 Z= 0.186 Angle : 0.629 9.073 18012 Z= 0.285 Chirality : 0.043 0.260 2096 Planarity : 0.004 0.041 2164 Dihedral : 16.408 162.613 2260 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.03 % Allowed : 17.61 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.23), residues: 1544 helix: 0.82 (0.19), residues: 892 sheet: -0.93 (0.52), residues: 88 loop : -1.24 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 264 HIS 0.001 0.000 HIS C 232 PHE 0.006 0.001 PHE A 309 TYR 0.009 0.001 TYR A 175 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 125 time to evaluate : 1.453 Fit side-chains REVERT: A 158 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 221 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (tp) REVERT: A 229 LYS cc_start: 0.8983 (tttp) cc_final: 0.8674 (tttt) REVERT: A 230 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 233 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7735 (mtp85) REVERT: A 272 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: B 158 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8913 (pp) REVERT: B 221 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 229 LYS cc_start: 0.9009 (tttp) cc_final: 0.8709 (tttt) REVERT: B 230 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8555 (tp) REVERT: B 272 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: C 158 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8912 (pp) REVERT: C 221 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8703 (tp) REVERT: C 230 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8516 (tp) REVERT: C 236 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 272 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: D 158 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8915 (pp) REVERT: D 221 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8700 (tp) REVERT: D 229 LYS cc_start: 0.8968 (tttp) cc_final: 0.8656 (tttt) REVERT: D 230 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 236 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8505 (p) REVERT: D 272 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7493 (tp30) outliers start: 54 outliers final: 23 residues processed: 175 average time/residue: 0.2537 time to fit residues: 65.5088 Evaluate side-chains 161 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13340 Z= 0.261 Angle : 0.657 9.139 18012 Z= 0.301 Chirality : 0.044 0.264 2096 Planarity : 0.004 0.040 2164 Dihedral : 16.425 162.565 2260 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.33 % Allowed : 17.69 % Favored : 77.99 % 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: -0.05 (0.23), residues: 1544 helix: 0.77 (0.18), residues: 908 sheet: -0.86 (0.53), residues: 88 loop : -1.18 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 264 HIS 0.002 0.001 HIS C 232 PHE 0.007 0.001 PHE D 365 TYR 0.011 0.001 TYR B 175 ARG 0.002 0.000 ARG D 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 118 time to evaluate : 1.380 Fit side-chains REVERT: A 221 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8698 (tp) REVERT: A 229 LYS cc_start: 0.9032 (tttp) cc_final: 0.8637 (tttt) REVERT: A 230 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8523 (tp) REVERT: A 233 ARG cc_start: 0.8072 (ttt90) cc_final: 0.7733 (mtp85) REVERT: A 272 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: B 221 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8700 (tp) REVERT: B 229 LYS cc_start: 0.9041 (tttp) cc_final: 0.8751 (tttt) REVERT: B 230 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (tp) REVERT: B 272 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: B 394 LYS cc_start: 0.8834 (tptp) cc_final: 0.8429 (tptt) REVERT: C 221 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (tp) REVERT: C 230 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8536 (tp) REVERT: C 236 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 272 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: D 221 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8699 (tp) REVERT: D 229 LYS cc_start: 0.9004 (tttp) cc_final: 0.8709 (tttt) REVERT: D 230 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8513 (tp) REVERT: D 236 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8625 (p) REVERT: D 272 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7492 (tp30) outliers start: 58 outliers final: 37 residues processed: 172 average time/residue: 0.2285 time to fit residues: 59.0734 Evaluate side-chains 169 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13340 Z= 0.183 Angle : 0.625 9.168 18012 Z= 0.283 Chirality : 0.042 0.261 2096 Planarity : 0.004 0.041 2164 Dihedral : 16.218 162.306 2260 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.73 % Allowed : 18.21 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.23), residues: 1544 helix: 1.10 (0.19), residues: 884 sheet: -0.82 (0.53), residues: 88 loop : -1.12 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.002 0.001 HIS A 232 PHE 0.005 0.001 PHE A 309 TYR 0.009 0.001 TYR A 175 ARG 0.002 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 120 time to evaluate : 1.477 Fit side-chains REVERT: A 221 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8696 (tp) REVERT: A 229 LYS cc_start: 0.8973 (tttp) cc_final: 0.8623 (tttt) REVERT: A 230 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 233 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7682 (mtp85) REVERT: A 272 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: A 394 LYS cc_start: 0.8725 (tptp) cc_final: 0.8172 (tptt) REVERT: A 398 ASP cc_start: 0.8374 (m-30) cc_final: 0.7884 (m-30) REVERT: B 221 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 229 LYS cc_start: 0.8972 (tttp) cc_final: 0.8620 (tttt) REVERT: B 230 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 272 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: C 221 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8680 (tp) REVERT: C 230 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 236 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 272 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: C 394 LYS cc_start: 0.8713 (tptp) cc_final: 0.8348 (tptt) REVERT: D 221 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8697 (tp) REVERT: D 229 LYS cc_start: 0.8979 (tttp) cc_final: 0.8697 (tttt) REVERT: D 230 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8553 (tp) REVERT: D 236 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8489 (p) REVERT: D 272 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: D 334 MET cc_start: 0.6991 (ttt) cc_final: 0.6717 (tpp) REVERT: D 394 LYS cc_start: 0.8759 (tptp) cc_final: 0.8382 (tptt) outliers start: 50 outliers final: 22 residues processed: 167 average time/residue: 0.2313 time to fit residues: 57.7314 Evaluate side-chains 156 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13340 Z= 0.179 Angle : 0.631 9.116 18012 Z= 0.284 Chirality : 0.042 0.264 2096 Planarity : 0.004 0.041 2164 Dihedral : 16.051 162.067 2260 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.69 % Allowed : 18.51 % Favored : 78.81 % 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: 0.42 (0.23), residues: 1544 helix: 1.16 (0.19), residues: 892 sheet: -0.81 (0.53), residues: 88 loop : -0.90 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.001 0.000 HIS A 232 PHE 0.005 0.001 PHE A 365 TYR 0.008 0.001 TYR C 175 ARG 0.002 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 1.532 Fit side-chains REVERT: A 221 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 229 LYS cc_start: 0.8959 (tttp) cc_final: 0.8606 (tttt) REVERT: A 230 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8527 (tp) REVERT: A 233 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7672 (mtp85) REVERT: A 272 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: A 334 MET cc_start: 0.7010 (ttt) cc_final: 0.6740 (tpp) REVERT: A 394 LYS cc_start: 0.8735 (tptp) cc_final: 0.8146 (tptt) REVERT: A 398 ASP cc_start: 0.8332 (m-30) cc_final: 0.7816 (m-30) REVERT: B 221 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8691 (tp) REVERT: B 229 LYS cc_start: 0.8968 (tttp) cc_final: 0.8614 (tttt) REVERT: B 230 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 272 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: B 334 MET cc_start: 0.7005 (ttt) cc_final: 0.6743 (tpp) REVERT: B 394 LYS cc_start: 0.8706 (tptp) cc_final: 0.8166 (tptt) REVERT: B 398 ASP cc_start: 0.8388 (m-30) cc_final: 0.7808 (m-30) REVERT: C 221 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8693 (tp) REVERT: C 230 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8553 (tp) REVERT: C 272 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: C 334 MET cc_start: 0.6997 (ttt) cc_final: 0.6730 (tpp) REVERT: C 394 LYS cc_start: 0.8751 (tptp) cc_final: 0.8212 (tptt) REVERT: C 398 ASP cc_start: 0.8326 (m-30) cc_final: 0.7833 (m-30) REVERT: D 221 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8689 (tp) REVERT: D 229 LYS cc_start: 0.8985 (tttp) cc_final: 0.8600 (tttt) REVERT: D 230 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8547 (tp) REVERT: D 272 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: D 334 MET cc_start: 0.6996 (ttt) cc_final: 0.6724 (tpp) REVERT: D 398 ASP cc_start: 0.8371 (m-30) cc_final: 0.8137 (m-30) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.2352 time to fit residues: 55.7303 Evaluate side-chains 158 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.147899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115608 restraints weight = 17486.695| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.06 r_work: 0.3012 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13340 Z= 0.160 Angle : 0.616 8.904 18012 Z= 0.277 Chirality : 0.042 0.264 2096 Planarity : 0.004 0.038 2164 Dihedral : 15.858 161.765 2260 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.39 % Allowed : 18.81 % Favored : 78.81 % 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: 0.60 (0.24), residues: 1544 helix: 1.27 (0.19), residues: 896 sheet: -0.81 (0.54), residues: 88 loop : -0.77 (0.30), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.002 0.000 HIS A 232 PHE 0.006 0.001 PHE A 365 TYR 0.007 0.001 TYR C 175 ARG 0.003 0.000 ARG C 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.36 seconds wall clock time: 45 minutes 43.18 seconds (2743.18 seconds total)