Starting phenix.real_space_refine on Thu Feb 15 16:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjq_7482/02_2024/6cjq_7482_updated.pdb" } resolution = 3.42 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8472 2.51 5 N 2068 2.21 5 O 2200 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 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 7.10, per 1000 atoms: 0.56 Number of scatterers: 12768 At special positions: 0 Unit cell: (106.322, 106.322, 120.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2200 8.00 N 2068 7.00 C 8472 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: 4.62 Conformation dependent library (CDL) restraints added in 2.2 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 56.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 Proline residue: A 31 - end of helix removed outlier: 3.712A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.861A pdb=" N LEU A 44 " --> pdb=" O SER A 41 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.524A pdb=" N LEU A 49 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 51 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 58 " --> pdb=" O ILE A 55 " (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 102 through 125 removed outlier: 3.949A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.865A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 181 removed outlier: 3.612A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 223 removed outlier: 3.822A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.580A pdb=" N HIS A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.638A 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 307 through 313 removed outlier: 3.857A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 405 through 414 removed outlier: 4.106A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 35 Proline residue: B 31 - end of helix removed outlier: 3.712A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.861A pdb=" N LEU B 44 " --> pdb=" O SER B 41 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 3.524A pdb=" N LEU B 49 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 51 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 58 " --> pdb=" O ILE B 55 " (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 102 through 125 removed outlier: 3.949A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.865A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 removed outlier: 3.612A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 223 removed outlier: 3.822A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.580A pdb=" N HIS B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.638A 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 307 through 313 removed outlier: 3.857A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 414 removed outlier: 4.106A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 35 Proline residue: C 31 - end of helix removed outlier: 3.712A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 62 removed outlier: 3.861A pdb=" N LEU C 44 " --> pdb=" O SER C 41 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 3.524A pdb=" N LEU C 49 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 51 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 58 " --> pdb=" O ILE C 55 " (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 102 through 125 removed outlier: 3.949A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.865A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 181 removed outlier: 3.612A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 3.822A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.580A pdb=" N HIS C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.638A 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 307 through 313 removed outlier: 3.857A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'C' and resid 405 through 414 removed outlier: 4.106A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 35 Proline residue: D 31 - end of helix removed outlier: 3.712A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 62 removed outlier: 3.861A pdb=" N LEU D 44 " --> pdb=" O SER D 41 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 3.524A pdb=" N LEU D 49 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE D 58 " --> pdb=" O ILE D 55 " (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 102 through 125 removed outlier: 3.949A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.865A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.612A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 223 removed outlier: 3.822A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.580A pdb=" N HIS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.638A 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 307 through 313 removed outlier: 3.857A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 414 removed outlier: 4.106A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) 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: 3.789A 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: 3.789A 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: 3.789A 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: 3.789A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1524 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: 3.44 Time building geometry restraints manager: 5.06 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: 3100 1.33 - 1.45: 2308 1.45 - 1.57: 7572 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 13028 Sorted by residual: bond pdb=" CG LEU B 43 " pdb=" CD2 LEU B 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU A 43 " pdb=" CD2 LEU A 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU C 43 " pdb=" CD2 LEU C 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU D 43 " pdb=" CD2 LEU D 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" C PRO C 300 " pdb=" N LEU C 301 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.30e+00 ... (remaining 13023 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.95: 368 105.95 - 112.98: 7008 112.98 - 120.02: 4996 120.02 - 127.06: 5116 127.06 - 134.09: 144 Bond angle restraints: 17632 Sorted by residual: angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 17627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 7516 19.81 - 39.63: 316 39.63 - 59.44: 48 59.44 - 79.26: 16 79.26 - 99.07: 4 Dihedral angle restraints: 7900 sinusoidal: 3288 harmonic: 4612 Sorted by residual: dihedral pdb=" CA ILE A 189 " pdb=" C ILE A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE B 189 " pdb=" C ILE B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE C 189 " pdb=" C ILE C 189 " pdb=" N THR C 190 " pdb=" CA THR C 190 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1724 0.083 - 0.165: 316 0.165 - 0.248: 24 0.248 - 0.330: 4 0.330 - 0.413: 4 Chirality restraints: 2072 Sorted by residual: 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 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 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 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 2069 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU C 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU B 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU A 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.019 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3700 2.82 - 3.34: 11548 3.34 - 3.86: 20708 3.86 - 4.38: 21968 4.38 - 4.90: 39410 Nonbonded interactions: 97334 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU A 65 " pdb=" NH2 ARG A 124 " model vdw 2.309 2.520 ... (remaining 97329 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' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'B' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'C' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'D' and (resid 10 through 415 or resid 501 or (resid 502 and (name C15 or \ name C16 or name C19 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27)) or resid 505 or (resid 506 and (name C15 \ or name C16 or name C17 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27)))) } 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: 1.040 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: 4.290 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.400 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.009 0.070 13028 Z= 0.595 Angle : 1.365 10.700 17632 Z= 0.671 Chirality : 0.064 0.413 2072 Planarity : 0.009 0.051 2156 Dihedral : 12.070 99.069 4924 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.60 % Allowed : 6.85 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1552 helix: -2.04 (0.14), residues: 916 sheet: -1.86 (0.47), residues: 88 loop : -2.32 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 264 HIS 0.005 0.002 HIS C 281 PHE 0.011 0.002 PHE B 366 TYR 0.026 0.003 TYR C 211 ARG 0.006 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 268 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 171 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 171 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8853 (tp) REVERT: D 171 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (tp) outliers start: 8 outliers final: 0 residues processed: 272 average time/residue: 0.3004 time to fit residues: 111.4257 Evaluate side-chains 131 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 364 GLN B 217 ASN B 364 GLN C 217 ASN C 364 GLN D 217 ASN D 364 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13028 Z= 0.196 Angle : 0.675 10.693 17632 Z= 0.317 Chirality : 0.041 0.142 2072 Planarity : 0.006 0.054 2156 Dihedral : 9.085 72.786 1972 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.65 % Allowed : 9.82 % Favored : 86.53 % 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: -1.35 (0.21), residues: 1552 helix: -0.31 (0.18), residues: 892 sheet: -1.40 (0.41), residues: 112 loop : -1.58 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 264 HIS 0.002 0.000 HIS B 281 PHE 0.008 0.001 PHE A 302 TYR 0.013 0.001 TYR D 128 ARG 0.006 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 307 GLU cc_start: 0.7979 (tp30) cc_final: 0.7614 (tp30) REVERT: B 158 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8834 (pp) REVERT: C 158 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8838 (pp) REVERT: C 230 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (mm) REVERT: D 158 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8852 (pp) REVERT: D 230 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (mm) REVERT: D 307 GLU cc_start: 0.7993 (tp30) cc_final: 0.7634 (tp30) outliers start: 49 outliers final: 11 residues processed: 177 average time/residue: 0.2159 time to fit residues: 58.5092 Evaluate side-chains 128 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 13028 Z= 0.388 Angle : 0.753 9.822 17632 Z= 0.351 Chirality : 0.046 0.163 2072 Planarity : 0.006 0.053 2156 Dihedral : 8.650 64.742 1964 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.57 % Allowed : 12.28 % Favored : 84.15 % 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: -0.73 (0.22), residues: 1552 helix: 0.18 (0.19), residues: 896 sheet: -0.91 (0.47), residues: 88 loop : -1.38 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 264 HIS 0.003 0.001 HIS B 281 PHE 0.009 0.002 PHE A 40 TYR 0.014 0.002 TYR D 390 ARG 0.004 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8905 (tp) REVERT: A 230 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8553 (mm) REVERT: B 158 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8876 (pp) REVERT: B 221 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8892 (tp) REVERT: C 158 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8880 (pp) REVERT: C 221 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8892 (tp) REVERT: C 230 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8530 (mm) REVERT: D 158 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (pp) REVERT: D 221 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8904 (tp) REVERT: D 230 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8522 (mm) outliers start: 48 outliers final: 24 residues processed: 171 average time/residue: 0.2289 time to fit residues: 58.9884 Evaluate side-chains 139 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13028 Z= 0.185 Angle : 0.652 9.696 17632 Z= 0.297 Chirality : 0.040 0.157 2072 Planarity : 0.004 0.047 2156 Dihedral : 7.467 45.770 1964 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.98 % Allowed : 13.47 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.23), residues: 1552 helix: 0.56 (0.19), residues: 888 sheet: -0.60 (0.49), residues: 88 loop : -1.15 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 264 HIS 0.001 0.000 HIS B 281 PHE 0.007 0.001 PHE D 397 TYR 0.008 0.001 TYR A 128 ARG 0.002 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: B 158 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8844 (pp) REVERT: C 26 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: C 158 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8843 (pp) REVERT: D 158 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8857 (pp) REVERT: D 313 ILE cc_start: 0.9204 (tp) cc_final: 0.8872 (tt) outliers start: 40 outliers final: 17 residues processed: 154 average time/residue: 0.2303 time to fit residues: 53.2123 Evaluate side-chains 128 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13028 Z= 0.180 Angle : 0.631 12.581 17632 Z= 0.285 Chirality : 0.040 0.169 2072 Planarity : 0.004 0.047 2156 Dihedral : 6.845 44.841 1964 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.98 % Allowed : 13.69 % Favored : 83.33 % 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: 0.13 (0.23), residues: 1552 helix: 0.84 (0.19), residues: 888 sheet: -0.52 (0.49), residues: 88 loop : -0.91 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS B 281 PHE 0.017 0.001 PHE A 397 TYR 0.008 0.001 TYR D 175 ARG 0.002 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: A 114 LYS cc_start: 0.8694 (tptp) cc_final: 0.8140 (tptp) REVERT: A 221 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 26 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8169 (m-10) REVERT: B 57 ASP cc_start: 0.8816 (t70) cc_final: 0.8371 (t0) REVERT: B 114 LYS cc_start: 0.8694 (tptp) cc_final: 0.8092 (tptp) REVERT: B 158 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 221 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8910 (tp) REVERT: C 26 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8258 (m-10) REVERT: C 114 LYS cc_start: 0.8705 (tptp) cc_final: 0.8111 (tptp) REVERT: C 158 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8815 (pp) REVERT: C 221 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8907 (tp) REVERT: D 26 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: D 158 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8817 (pp) REVERT: D 221 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8914 (tp) REVERT: D 313 ILE cc_start: 0.9218 (tp) cc_final: 0.8867 (tt) outliers start: 40 outliers final: 18 residues processed: 164 average time/residue: 0.2410 time to fit residues: 58.5681 Evaluate side-chains 140 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13028 Z= 0.133 Angle : 0.599 10.794 17632 Z= 0.268 Chirality : 0.039 0.173 2072 Planarity : 0.004 0.049 2156 Dihedral : 6.190 43.808 1964 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.53 % Allowed : 15.48 % Favored : 81.99 % 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: 0.42 (0.23), residues: 1552 helix: 1.05 (0.19), residues: 892 sheet: -0.53 (0.48), residues: 88 loop : -0.72 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.000 0.000 HIS D 281 PHE 0.010 0.001 PHE A 397 TYR 0.006 0.001 TYR C 175 ARG 0.002 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8245 (m-10) REVERT: A 221 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8938 (tp) REVERT: B 26 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8229 (m-10) REVERT: B 57 ASP cc_start: 0.8790 (t70) cc_final: 0.8337 (t0) REVERT: B 221 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8938 (tp) REVERT: B 313 ILE cc_start: 0.9194 (tp) cc_final: 0.8809 (tt) REVERT: C 26 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8300 (m-10) REVERT: C 114 LYS cc_start: 0.8650 (tptp) cc_final: 0.8115 (tptp) REVERT: C 221 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8937 (tp) REVERT: C 229 LYS cc_start: 0.9269 (tttt) cc_final: 0.9050 (ttpt) REVERT: C 313 ILE cc_start: 0.9191 (tp) cc_final: 0.8805 (tt) REVERT: D 26 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: D 221 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8938 (tp) REVERT: D 313 ILE cc_start: 0.9202 (tp) cc_final: 0.8838 (tt) outliers start: 34 outliers final: 19 residues processed: 161 average time/residue: 0.2239 time to fit residues: 54.1104 Evaluate side-chains 137 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13028 Z= 0.134 Angle : 0.622 11.311 17632 Z= 0.272 Chirality : 0.039 0.183 2072 Planarity : 0.004 0.050 2156 Dihedral : 5.871 44.196 1964 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.53 % Allowed : 15.62 % Favored : 81.85 % 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: 0.65 (0.23), residues: 1552 helix: 1.22 (0.19), residues: 892 sheet: -0.42 (0.49), residues: 88 loop : -0.61 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS C 99 PHE 0.009 0.001 PHE A 397 TYR 0.006 0.001 TYR B 175 ARG 0.002 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: A 221 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 26 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8276 (m-10) REVERT: B 57 ASP cc_start: 0.8738 (t70) cc_final: 0.8265 (t0) REVERT: B 221 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8941 (tp) REVERT: B 313 ILE cc_start: 0.9178 (tp) cc_final: 0.8770 (tt) REVERT: C 26 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: C 114 LYS cc_start: 0.8617 (tptp) cc_final: 0.8129 (tptp) REVERT: C 221 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8938 (tp) REVERT: C 313 ILE cc_start: 0.9173 (tp) cc_final: 0.8749 (tt) REVERT: D 26 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: D 221 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8944 (tp) REVERT: D 229 LYS cc_start: 0.9260 (tttt) cc_final: 0.9045 (ttpt) REVERT: D 313 ILE cc_start: 0.9205 (tp) cc_final: 0.8840 (tt) outliers start: 34 outliers final: 20 residues processed: 149 average time/residue: 0.2260 time to fit residues: 51.6646 Evaluate side-chains 137 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13028 Z= 0.320 Angle : 0.693 10.959 17632 Z= 0.317 Chirality : 0.043 0.203 2072 Planarity : 0.005 0.048 2156 Dihedral : 6.799 49.615 1964 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.98 % Allowed : 16.82 % Favored : 80.21 % 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: 0.55 (0.23), residues: 1552 helix: 1.05 (0.19), residues: 920 sheet: -0.41 (0.50), residues: 88 loop : -0.57 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 176 HIS 0.003 0.001 HIS D 281 PHE 0.007 0.001 PHE D 174 TYR 0.015 0.001 TYR C 390 ARG 0.002 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 116 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: A 221 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8879 (tp) REVERT: B 26 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: B 221 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8873 (tp) REVERT: B 313 ILE cc_start: 0.9191 (tp) cc_final: 0.8884 (tt) REVERT: C 26 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: C 221 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (tp) REVERT: C 313 ILE cc_start: 0.9199 (tp) cc_final: 0.8889 (tt) REVERT: D 26 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: D 221 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8881 (tp) REVERT: D 313 ILE cc_start: 0.9207 (tp) cc_final: 0.8940 (tt) outliers start: 40 outliers final: 26 residues processed: 146 average time/residue: 0.2592 time to fit residues: 55.0125 Evaluate side-chains 145 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL 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: 1.9990 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13028 Z= 0.152 Angle : 0.641 11.089 17632 Z= 0.286 Chirality : 0.040 0.214 2072 Planarity : 0.004 0.051 2156 Dihedral : 6.098 49.440 1964 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.46 % Allowed : 17.11 % Favored : 80.43 % 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: 0.74 (0.23), residues: 1552 helix: 1.17 (0.19), residues: 920 sheet: -0.29 (0.51), residues: 88 loop : -0.44 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS B 281 PHE 0.010 0.001 PHE A 397 TYR 0.008 0.001 TYR A 175 ARG 0.013 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.411 Fit side-chains REVERT: A 26 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: A 221 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8896 (tp) REVERT: B 26 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: B 221 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8888 (tp) REVERT: B 313 ILE cc_start: 0.9186 (tp) cc_final: 0.8816 (tt) REVERT: C 26 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: C 114 LYS cc_start: 0.8743 (tptp) cc_final: 0.8172 (tptp) REVERT: C 221 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8886 (tp) REVERT: C 313 ILE cc_start: 0.9203 (tp) cc_final: 0.8860 (tt) REVERT: D 26 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8271 (m-10) REVERT: D 221 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8889 (tp) REVERT: D 313 ILE cc_start: 0.9197 (tp) cc_final: 0.8825 (tt) REVERT: D 410 GLN cc_start: 0.8010 (pt0) cc_final: 0.7776 (pt0) outliers start: 33 outliers final: 22 residues processed: 144 average time/residue: 0.2568 time to fit residues: 53.9853 Evaluate side-chains 140 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13028 Z= 0.173 Angle : 0.638 11.848 17632 Z= 0.286 Chirality : 0.040 0.218 2072 Planarity : 0.004 0.061 2156 Dihedral : 5.924 49.717 1964 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.38 % Allowed : 17.11 % Favored : 80.51 % 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: 0.81 (0.23), residues: 1552 helix: 1.22 (0.19), residues: 924 sheet: -0.19 (0.51), residues: 88 loop : -0.42 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 264 HIS 0.001 0.000 HIS D 281 PHE 0.009 0.001 PHE A 397 TYR 0.008 0.001 TYR A 175 ARG 0.011 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8300 (m-10) REVERT: A 221 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8908 (tp) REVERT: A 229 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8967 (ttmt) REVERT: B 26 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (m-10) REVERT: B 221 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8907 (tp) REVERT: B 313 ILE cc_start: 0.9182 (tp) cc_final: 0.8808 (tt) REVERT: C 26 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: C 114 LYS cc_start: 0.8703 (tptp) cc_final: 0.8133 (tptp) REVERT: C 221 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (tp) REVERT: C 313 ILE cc_start: 0.9181 (tp) cc_final: 0.8801 (tt) REVERT: D 26 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (m-10) REVERT: D 221 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8907 (tp) REVERT: D 229 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8854 (ttmt) REVERT: D 313 ILE cc_start: 0.9187 (tp) cc_final: 0.8817 (tt) outliers start: 32 outliers final: 23 residues processed: 140 average time/residue: 0.2675 time to fit residues: 54.1009 Evaluate side-chains 143 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.120273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091807 restraints weight = 23100.254| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.22 r_work: 0.3021 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13028 Z= 0.160 Angle : 0.635 12.211 17632 Z= 0.283 Chirality : 0.040 0.216 2072 Planarity : 0.004 0.053 2156 Dihedral : 5.693 50.691 1964 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.83 % Allowed : 17.34 % Favored : 79.84 % 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: 0.90 (0.23), residues: 1552 helix: 1.32 (0.19), residues: 924 sheet: -0.23 (0.51), residues: 88 loop : -0.42 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS B 281 PHE 0.009 0.001 PHE A 397 TYR 0.007 0.001 TYR A 175 ARG 0.008 0.000 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.98 seconds wall clock time: 45 minutes 17.09 seconds (2717.09 seconds total)