Starting phenix.real_space_refine on Sun Mar 17 22:08:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/03_2024/7ryr_24746_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6124 atoms to isotropic. 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 8636 2.51 5 N 2080 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 413": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13024 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "C" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "B" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 7.25, per 1000 atoms: 0.56 Number of scatterers: 13024 At special positions: 0 Unit cell: (108.009, 108.009, 113.464, 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 2272 8.00 N 2080 7.00 C 8636 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: 5.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 8 sheets defined 56.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 35 removed outlier: 3.895A pdb=" N VAL A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.690A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 102 through 118 removed outlier: 4.255A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.637A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 223 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.569A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.951A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'C' and resid 12 through 35 removed outlier: 3.895A pdb=" N VAL C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.690A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 95 through 98 No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 102 through 118 removed outlier: 4.256A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.637A pdb=" N LEU C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 210 through 223 Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.569A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.951A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'D' and resid 12 through 35 removed outlier: 3.895A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 56 removed outlier: 3.690A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 102 through 121 removed outlier: 4.255A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.638A pdb=" N LEU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 223 Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.569A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.951A pdb=" N ARG D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'B' and resid 12 through 35 removed outlier: 3.896A pdb=" N VAL B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.689A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 95 through 98 No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 102 through 118 removed outlier: 4.255A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.637A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 223 Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.569A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.951A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 405 through 417 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.211A pdb=" N TYR A 390 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE A 341 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 392 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR A 339 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 318 through 322 removed outlier: 6.211A pdb=" N TYR C 390 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE C 341 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 392 " --> pdb=" O TYR C 339 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR C 339 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.211A pdb=" N TYR D 390 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE D 341 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 392 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR D 339 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.212A pdb=" N TYR B 390 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE B 341 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 392 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 339 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1599 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: 3.28 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2014 1.32 - 1.44: 3298 1.44 - 1.56: 7900 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13280 Sorted by residual: bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" CA SER C 157 " pdb=" CB SER C 157 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 ... (remaining 13275 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.68: 604 107.68 - 114.81: 7914 114.81 - 121.94: 6972 121.94 - 129.07: 2354 129.07 - 136.19: 92 Bond angle restraints: 17936 Sorted by residual: angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.83e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 111.82 104.67 7.15 1.16e+00 7.43e-01 3.80e+01 angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 111.82 104.70 7.12 1.16e+00 7.43e-01 3.77e+01 angle pdb=" CA ASP C 92 " pdb=" C ASP C 92 " pdb=" O ASP C 92 " ideal model delta sigma weight residual 121.56 115.40 6.16 1.09e+00 8.42e-01 3.19e+01 ... (remaining 17931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 7872 35.02 - 70.04: 192 70.04 - 105.06: 20 105.06 - 140.08: 32 140.08 - 175.10: 12 Dihedral angle restraints: 8128 sinusoidal: 3560 harmonic: 4568 Sorted by residual: dihedral pdb=" C01 PGW C 502 " pdb=" C19 PGW C 502 " pdb=" O03 PGW C 502 " pdb=" O04 PGW C 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.10 175.10 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW A 502 " pdb=" C19 PGW A 502 " pdb=" O03 PGW A 502 " pdb=" O04 PGW A 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.08 175.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW D 502 " pdb=" C19 PGW D 502 " pdb=" O03 PGW D 502 " pdb=" O04 PGW D 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.06 175.06 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1857 0.087 - 0.175: 195 0.175 - 0.262: 32 0.262 - 0.350: 4 0.350 - 0.437: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA LYS D 246 " pdb=" N LYS D 246 " pdb=" C LYS D 246 " pdb=" CB LYS D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2089 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.091 2.00e-02 2.50e+03 9.04e-02 8.17e+01 pdb=" C10 PGW B 503 " -0.091 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.090 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW D 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW D 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW D 503 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW A 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " 0.090 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 12877 3.28 - 3.82: 19764 3.82 - 4.36: 23705 4.36 - 4.90: 41054 Nonbonded interactions: 98259 Sorted by model distance: nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.198 2.440 nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.198 2.440 nonbonded pdb=" O GLN D 119 " pdb=" OG1 THR D 123 " model vdw 2.245 2.440 ... (remaining 98254 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 420 or resid 501 through 506 or (resid 507 and \ (name C15 or name C16 or name C17 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)))) selection = (chain 'B' and (resid 10 through 420 or resid 501 through 505 or (resid 506 and \ (name C15 or name C16 or name C17 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27)) or (resid 507 and (name C15 or name C16 or name C17 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or resid 501 through 506 or (resid 507 and \ (name C15 or name C16 or name C17 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)))) selection = (chain 'D' and (resid 10 through 420 or resid 501 through 505 or (resid 506 and \ (name C15 or name C16 or name C17 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27)) or (resid 507 and (name C15 or name C16 or name C17 \ 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 3.650 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 36.750 Find NCS groups from input model: 0.890 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: 0.010 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.007 0.176 13280 Z= 0.458 Angle : 1.118 13.029 17936 Z= 0.649 Chirality : 0.059 0.437 2092 Planarity : 0.008 0.090 2168 Dihedral : 19.137 175.101 5176 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.60 % Allowed : 1.50 % Favored : 97.90 % Cbeta Deviations : 0.27 % 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: -1.65 (0.22), residues: 1532 helix: -0.52 (0.17), residues: 988 sheet: -1.63 (0.47), residues: 132 loop : -1.98 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS B 149 PHE 0.019 0.002 PHE C 365 TYR 0.023 0.001 TYR A 26 ARG 0.011 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 1.345 Fit side-chains REVERT: A 334 MET cc_start: 0.5592 (tmm) cc_final: 0.5245 (tmm) REVERT: C 110 VAL cc_start: 0.8653 (m) cc_final: 0.8428 (p) REVERT: C 289 MET cc_start: 0.8365 (mmm) cc_final: 0.8148 (mmm) REVERT: D 110 VAL cc_start: 0.8688 (m) cc_final: 0.8441 (p) outliers start: 8 outliers final: 4 residues processed: 243 average time/residue: 0.1841 time to fit residues: 70.5285 Evaluate side-chains 192 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain B residue 92 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 GLN B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13280 Z= 0.182 Angle : 0.673 9.997 17936 Z= 0.316 Chirality : 0.041 0.142 2092 Planarity : 0.006 0.063 2168 Dihedral : 17.305 135.219 2236 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.25 % Allowed : 8.56 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1532 helix: -0.13 (0.17), residues: 1008 sheet: -1.58 (0.46), residues: 132 loop : -2.04 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 155 HIS 0.003 0.001 HIS B 292 PHE 0.031 0.001 PHE B 40 TYR 0.016 0.001 TYR A 25 ARG 0.004 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.562 Fit side-chains REVERT: A 266 THR cc_start: 0.8549 (t) cc_final: 0.8334 (t) REVERT: B 25 TYR cc_start: 0.8115 (t80) cc_final: 0.7886 (t80) outliers start: 30 outliers final: 15 residues processed: 218 average time/residue: 0.1903 time to fit residues: 66.3775 Evaluate side-chains 198 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13280 Z= 0.257 Angle : 0.666 10.723 17936 Z= 0.313 Chirality : 0.041 0.141 2092 Planarity : 0.005 0.063 2168 Dihedral : 15.648 130.949 2230 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.78 % Allowed : 12.91 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.22), residues: 1532 helix: 0.19 (0.18), residues: 996 sheet: -1.86 (0.47), residues: 124 loop : -1.92 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.003 0.001 HIS D 292 PHE 0.027 0.001 PHE B 40 TYR 0.013 0.001 TYR C 175 ARG 0.007 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.595 Fit side-chains REVERT: C 290 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: D 221 LEU cc_start: 0.8208 (mp) cc_final: 0.8003 (mt) REVERT: D 290 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: D 334 MET cc_start: 0.6341 (tmm) cc_final: 0.5948 (tmm) REVERT: B 221 LEU cc_start: 0.8169 (mp) cc_final: 0.7964 (mt) REVERT: B 290 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6735 (mp0) outliers start: 37 outliers final: 20 residues processed: 213 average time/residue: 0.1956 time to fit residues: 65.2348 Evaluate side-chains 197 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13280 Z= 0.149 Angle : 0.614 10.141 17936 Z= 0.286 Chirality : 0.039 0.140 2092 Planarity : 0.005 0.058 2168 Dihedral : 14.210 130.853 2228 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.08 % Allowed : 14.56 % Favored : 82.36 % 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: -0.56 (0.23), residues: 1532 helix: 0.47 (0.18), residues: 996 sheet: -1.79 (0.46), residues: 124 loop : -1.82 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 264 HIS 0.003 0.001 HIS B 99 PHE 0.021 0.001 PHE C 40 TYR 0.016 0.001 TYR B 25 ARG 0.006 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.458 Fit side-chains REVERT: A 389 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7995 (pp) REVERT: C 290 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: C 389 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8339 (pp) REVERT: D 290 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: D 389 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 221 LEU cc_start: 0.8155 (mp) cc_final: 0.7902 (mt) REVERT: B 290 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: B 389 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8353 (pp) outliers start: 41 outliers final: 22 residues processed: 215 average time/residue: 0.1954 time to fit residues: 66.1121 Evaluate side-chains 198 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.0030 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13280 Z= 0.166 Angle : 0.613 9.484 17936 Z= 0.285 Chirality : 0.039 0.134 2092 Planarity : 0.005 0.058 2168 Dihedral : 13.145 130.928 2228 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.83 % Allowed : 15.77 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.23), residues: 1532 helix: 0.66 (0.18), residues: 1000 sheet: -1.77 (0.46), residues: 124 loop : -1.74 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.002 0.001 HIS A 292 PHE 0.018 0.001 PHE A 40 TYR 0.011 0.001 TYR B 25 ARG 0.007 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 179 time to evaluate : 1.451 Fit side-chains REVERT: A 389 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8072 (pp) REVERT: C 289 MET cc_start: 0.8278 (mmm) cc_final: 0.8020 (mmm) REVERT: C 290 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: C 389 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8133 (pp) REVERT: D 119 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.5931 (pm20) REVERT: D 290 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 389 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 221 LEU cc_start: 0.8113 (mp) cc_final: 0.7897 (mt) REVERT: B 290 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 389 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8456 (pp) outliers start: 51 outliers final: 32 residues processed: 215 average time/residue: 0.1856 time to fit residues: 64.5075 Evaluate side-chains 210 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13280 Z= 0.150 Angle : 0.602 9.134 17936 Z= 0.278 Chirality : 0.039 0.135 2092 Planarity : 0.005 0.055 2168 Dihedral : 12.492 130.767 2228 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.35 % Allowed : 15.84 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.23), residues: 1532 helix: 0.85 (0.18), residues: 1004 sheet: -1.70 (0.46), residues: 124 loop : -1.66 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 264 HIS 0.003 0.001 HIS B 99 PHE 0.026 0.001 PHE B 40 TYR 0.011 0.001 TYR B 25 ARG 0.006 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 1.452 Fit side-chains REVERT: A 389 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8088 (pp) REVERT: C 290 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: C 318 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: C 389 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8124 (pp) REVERT: D 119 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.5666 (pm20) REVERT: D 289 MET cc_start: 0.8357 (mmm) cc_final: 0.8124 (mmm) REVERT: D 290 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: D 318 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: D 389 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8147 (pp) REVERT: B 389 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8270 (pp) outliers start: 58 outliers final: 37 residues processed: 221 average time/residue: 0.1820 time to fit residues: 64.5832 Evaluate side-chains 216 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 89 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13280 Z= 0.141 Angle : 0.610 9.292 17936 Z= 0.279 Chirality : 0.039 0.143 2092 Planarity : 0.005 0.054 2168 Dihedral : 11.983 130.744 2228 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.90 % Allowed : 17.27 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.24), residues: 1532 helix: 1.00 (0.18), residues: 1000 sheet: -1.69 (0.46), residues: 124 loop : -1.47 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 264 HIS 0.002 0.000 HIS B 281 PHE 0.017 0.001 PHE A 40 TYR 0.010 0.001 TYR B 25 ARG 0.007 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 180 time to evaluate : 1.450 Fit side-chains REVERT: A 389 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8088 (pp) REVERT: C 290 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 318 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: C 389 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8105 (pp) REVERT: D 119 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: D 164 ASN cc_start: 0.8987 (m-40) cc_final: 0.8727 (t0) REVERT: D 290 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: D 389 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8126 (pp) REVERT: B 290 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 389 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 410 GLN cc_start: 0.8269 (tp40) cc_final: 0.8063 (tp-100) outliers start: 52 outliers final: 39 residues processed: 217 average time/residue: 0.1945 time to fit residues: 66.5294 Evaluate side-chains 211 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 140 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7956 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13280 Z= 0.154 Angle : 0.614 8.954 17936 Z= 0.280 Chirality : 0.039 0.130 2092 Planarity : 0.005 0.054 2168 Dihedral : 11.809 130.776 2228 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.13 % Allowed : 17.87 % Favored : 78.00 % 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: 0.29 (0.24), residues: 1532 helix: 1.21 (0.18), residues: 976 sheet: -1.68 (0.46), residues: 124 loop : -1.52 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 264 HIS 0.002 0.001 HIS B 99 PHE 0.018 0.001 PHE A 40 TYR 0.010 0.001 TYR B 25 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 1.346 Fit side-chains REVERT: A 389 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8311 (pp) REVERT: C 290 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: C 318 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: C 389 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8371 (pp) REVERT: D 119 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: D 164 ASN cc_start: 0.8992 (m-40) cc_final: 0.8735 (t0) REVERT: D 290 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: D 318 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: D 389 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8381 (pp) REVERT: B 289 MET cc_start: 0.8267 (mmm) cc_final: 0.8060 (mmm) REVERT: B 290 GLU cc_start: 0.7345 (mp0) cc_final: 0.7034 (mp0) REVERT: B 389 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8106 (pp) REVERT: B 410 GLN cc_start: 0.8262 (tp40) cc_final: 0.8035 (tp-100) outliers start: 55 outliers final: 44 residues processed: 212 average time/residue: 0.1731 time to fit residues: 60.7769 Evaluate side-chains 220 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 167 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 140 optimal weight: 0.0040 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 144 optimal weight: 0.7980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13280 Z= 0.144 Angle : 0.610 8.986 17936 Z= 0.278 Chirality : 0.039 0.136 2092 Planarity : 0.005 0.055 2168 Dihedral : 11.579 130.760 2228 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.05 % Allowed : 17.94 % Favored : 78.00 % 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: 0.29 (0.24), residues: 1532 helix: 1.10 (0.18), residues: 1000 sheet: -1.65 (0.47), residues: 124 loop : -1.38 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 15 HIS 0.001 0.000 HIS C 292 PHE 0.016 0.001 PHE A 40 TYR 0.009 0.001 TYR B 25 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 1.551 Fit side-chains REVERT: A 289 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7788 (mmm) REVERT: A 389 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 164 ASN cc_start: 0.9006 (m-40) cc_final: 0.8777 (t0) REVERT: C 290 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: C 318 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: C 389 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8367 (pp) REVERT: D 119 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5646 (pm20) REVERT: D 164 ASN cc_start: 0.8980 (m-40) cc_final: 0.8729 (t0) REVERT: D 290 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: D 318 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: D 389 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 389 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8098 (pp) REVERT: B 410 GLN cc_start: 0.8260 (tp40) cc_final: 0.8040 (tp-100) outliers start: 54 outliers final: 40 residues processed: 211 average time/residue: 0.1808 time to fit residues: 62.1173 Evaluate side-chains 215 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 0.0020 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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: 0.7950 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13280 Z= 0.155 Angle : 0.617 8.604 17936 Z= 0.282 Chirality : 0.039 0.129 2092 Planarity : 0.005 0.056 2168 Dihedral : 11.211 130.782 2228 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.98 % Allowed : 17.64 % Favored : 78.38 % 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: 0.43 (0.24), residues: 1532 helix: 1.31 (0.18), residues: 976 sheet: -1.60 (0.47), residues: 124 loop : -1.44 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 15 HIS 0.002 0.000 HIS A 292 PHE 0.019 0.001 PHE A 40 TYR 0.009 0.001 TYR B 25 ARG 0.002 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 1.446 Fit side-chains REVERT: A 289 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: A 389 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8303 (pp) REVERT: C 164 ASN cc_start: 0.9010 (m-40) cc_final: 0.8782 (t0) REVERT: C 290 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: C 318 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: C 389 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8385 (pp) REVERT: D 119 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: D 164 ASN cc_start: 0.8991 (m-40) cc_final: 0.8741 (t0) REVERT: D 290 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: D 318 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: D 389 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 290 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 389 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8108 (pp) REVERT: B 410 GLN cc_start: 0.8267 (tp40) cc_final: 0.8040 (tp-100) outliers start: 53 outliers final: 38 residues processed: 206 average time/residue: 0.1736 time to fit residues: 59.1996 Evaluate side-chains 215 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.159781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123723 restraints weight = 17297.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111829 restraints weight = 22071.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111279 restraints weight = 20004.729| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.002 0.025 13280 Z= 0.151 Angle : 0.620 8.861 17936 Z= 0.281 Chirality : 0.039 0.132 2092 Planarity : 0.005 0.056 2168 Dihedral : 10.952 130.743 2228 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.90 % Allowed : 18.09 % Favored : 78.00 % 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: 0.39 (0.23), residues: 1532 helix: 1.18 (0.18), residues: 1000 sheet: -1.55 (0.48), residues: 124 loop : -1.36 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 15 HIS 0.001 0.000 HIS D 99 PHE 0.015 0.001 PHE A 40 TYR 0.009 0.001 TYR B 25 ARG 0.002 0.000 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.38 seconds wall clock time: 46 minutes 58.50 seconds (2818.50 seconds total)