Starting phenix.real_space_refine on Sun Nov 17 04:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/11_2024/8d66_27218_neut.cif" } resolution = 3.14 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 35 5.16 5 C 8375 2.51 5 N 2085 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.32, per 1000 atoms: 0.42 Number of scatterers: 12800 At special positions: 0 Unit cell: (90.2, 90.2, 125.4, 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 35 16.00 P 5 15.00 O 2300 8.00 N 2085 7.00 C 8375 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 34.1% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.542A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.542A pdb=" N ILE A 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 201 through 209 removed outlier: 3.860A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.682A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.541A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.543A pdb=" N ILE B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 201 through 209 removed outlier: 3.860A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.681A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.541A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.542A pdb=" N ILE C 152 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 153 " --> pdb=" O GLU C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 201 through 209 removed outlier: 3.861A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 249 Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.681A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.541A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.542A pdb=" N ILE D 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 153' Processing helix chain 'D' and resid 201 through 209 removed outlier: 3.861A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 249 Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.682A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.541A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.542A pdb=" N ILE E 152 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 153 " --> pdb=" O GLU E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 153' Processing helix chain 'E' and resid 201 through 209 removed outlier: 3.860A pdb=" N ILE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 249 Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.681A pdb=" N LEU E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.238A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 42 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A 196 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS A 165 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 198 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 163 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.237A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 42 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP B 196 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 165 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 198 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG B 163 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.237A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 42 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP C 196 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS C 165 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C 198 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG C 163 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.237A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 42 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP D 196 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS D 165 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D 198 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG D 163 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.237A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 42 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP E 196 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS E 165 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL E 198 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG E 163 " --> pdb=" O VAL E 198 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1650 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: 3.91 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2021 1.31 - 1.43: 3759 1.43 - 1.56: 7285 1.56 - 1.68: 10 1.68 - 1.81: 55 Bond restraints: 13130 Sorted by residual: bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 PGW E 401 " pdb=" O01 PGW E 401 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 13125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 17160 2.34 - 4.69: 550 4.69 - 7.03: 95 7.03 - 9.38: 5 9.38 - 11.72: 15 Bond angle restraints: 17825 Sorted by residual: angle pdb=" O11 PGW C 401 " pdb=" P PGW C 401 " pdb=" O12 PGW C 401 " ideal model delta sigma weight residual 98.90 110.62 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PGW A 401 " pdb=" P PGW A 401 " pdb=" O12 PGW A 401 " ideal model delta sigma weight residual 98.90 110.59 -11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW B 401 " pdb=" P PGW B 401 " pdb=" O12 PGW B 401 " ideal model delta sigma weight residual 98.90 110.58 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW E 401 " pdb=" P PGW E 401 " pdb=" O12 PGW E 401 " ideal model delta sigma weight residual 98.90 110.58 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW D 401 " pdb=" P PGW D 401 " pdb=" O12 PGW D 401 " ideal model delta sigma weight residual 98.90 110.56 -11.66 3.00e+00 1.11e-01 1.51e+01 ... (remaining 17820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 7531 34.71 - 69.42: 184 69.42 - 104.12: 20 104.12 - 138.83: 25 138.83 - 173.54: 5 Dihedral angle restraints: 7765 sinusoidal: 3260 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU E 118 " pdb=" C LEU E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 7762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1385 0.057 - 0.115: 438 0.115 - 0.172: 107 0.172 - 0.230: 25 0.230 - 0.287: 5 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA THR B 61 " pdb=" N THR B 61 " pdb=" C THR B 61 " pdb=" CB THR B 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA THR E 61 " pdb=" N THR E 61 " pdb=" C THR E 61 " pdb=" CB THR E 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1957 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 206 " 0.021 2.00e-02 2.50e+03 1.65e-02 6.80e+00 pdb=" CG TRP D 206 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 206 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 206 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 206 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 206 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 206 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 206 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 206 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.021 2.00e-02 2.50e+03 1.65e-02 6.78e+00 pdb=" CG TRP A 206 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 206 " -0.021 2.00e-02 2.50e+03 1.64e-02 6.70e+00 pdb=" CG TRP E 206 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 206 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 206 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 206 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 206 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 206 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 206 " -0.011 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3871 2.83 - 3.35: 10813 3.35 - 3.86: 20302 3.86 - 4.38: 24375 4.38 - 4.90: 42848 Nonbonded interactions: 102209 Sorted by model distance: nonbonded pdb=" O SER D 221 " pdb=" OG SER D 221 " model vdw 2.309 3.040 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.309 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.309 3.040 ... (remaining 102204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.450 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 13130 Z= 0.588 Angle : 1.018 11.720 17825 Z= 0.512 Chirality : 0.061 0.287 1960 Planarity : 0.005 0.039 2250 Dihedral : 18.545 173.540 4855 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1525 helix: -0.19 (0.22), residues: 515 sheet: 0.28 (0.28), residues: 395 loop : -2.85 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 206 HIS 0.004 0.002 HIS A 177 PHE 0.016 0.002 PHE D 228 TYR 0.023 0.003 TYR D 245 ARG 0.007 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8835 (mttt) cc_final: 0.8462 (mtmt) REVERT: A 86 ASP cc_start: 0.7856 (t0) cc_final: 0.7374 (t70) REVERT: A 174 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7352 (ttt-90) REVERT: B 54 LYS cc_start: 0.8558 (mttt) cc_final: 0.8270 (mtmt) REVERT: B 65 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7151 (mtm180) REVERT: B 86 ASP cc_start: 0.7812 (t0) cc_final: 0.7449 (t70) REVERT: B 90 LYS cc_start: 0.8884 (pttt) cc_final: 0.8651 (ptpp) REVERT: C 114 MET cc_start: 0.9024 (mtt) cc_final: 0.8761 (mtt) REVERT: C 265 MET cc_start: 0.8348 (mtp) cc_final: 0.8076 (mtp) REVERT: D 86 ASP cc_start: 0.7720 (t0) cc_final: 0.7269 (t70) REVERT: D 113 ASP cc_start: 0.7273 (m-30) cc_final: 0.7059 (p0) REVERT: E 21 ASN cc_start: 0.8540 (t0) cc_final: 0.8186 (t0) REVERT: E 54 LYS cc_start: 0.8752 (mttt) cc_final: 0.8133 (mtpp) REVERT: E 86 ASP cc_start: 0.7912 (t0) cc_final: 0.7397 (t70) REVERT: E 113 ASP cc_start: 0.7200 (m-30) cc_final: 0.6796 (p0) REVERT: E 174 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7351 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3169 time to fit residues: 70.0011 Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN C 27 ASN D 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13130 Z= 0.196 Angle : 0.559 5.277 17825 Z= 0.285 Chirality : 0.047 0.174 1960 Planarity : 0.004 0.036 2250 Dihedral : 14.726 91.858 1925 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.16 % Allowed : 4.95 % Favored : 93.89 % 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: -0.76 (0.22), residues: 1525 helix: 0.97 (0.24), residues: 515 sheet: 0.54 (0.28), residues: 395 loop : -2.61 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 206 HIS 0.002 0.001 HIS A 177 PHE 0.011 0.001 PHE D 236 TYR 0.015 0.001 TYR C 245 ARG 0.002 0.000 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.405 Fit side-chains REVERT: A 21 ASN cc_start: 0.8121 (t0) cc_final: 0.7920 (t0) REVERT: A 54 LYS cc_start: 0.8810 (mttt) cc_final: 0.8484 (mtmt) REVERT: A 86 ASP cc_start: 0.7805 (t0) cc_final: 0.7349 (t70) REVERT: A 223 PHE cc_start: 0.8346 (m-80) cc_final: 0.7795 (m-80) REVERT: A 245 TYR cc_start: 0.7697 (m-80) cc_final: 0.7058 (m-80) REVERT: B 54 LYS cc_start: 0.8455 (mttt) cc_final: 0.8233 (mtmt) REVERT: B 65 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7250 (mtm180) REVERT: B 86 ASP cc_start: 0.7775 (t0) cc_final: 0.7445 (t70) REVERT: C 265 MET cc_start: 0.8195 (mtp) cc_final: 0.7796 (mtp) REVERT: D 86 ASP cc_start: 0.7679 (t0) cc_final: 0.7204 (t70) REVERT: D 113 ASP cc_start: 0.7310 (m-30) cc_final: 0.7018 (p0) REVERT: E 21 ASN cc_start: 0.8225 (t0) cc_final: 0.7966 (t0) REVERT: E 86 ASP cc_start: 0.7808 (t0) cc_final: 0.7373 (t70) REVERT: E 114 MET cc_start: 0.9105 (mtt) cc_final: 0.8689 (mtt) REVERT: E 174 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7647 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 148 average time/residue: 0.2933 time to fit residues: 60.7137 Evaluate side-chains 129 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 124 GLN D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13130 Z= 0.187 Angle : 0.520 5.700 17825 Z= 0.266 Chirality : 0.047 0.200 1960 Planarity : 0.004 0.029 2250 Dihedral : 12.684 86.332 1925 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.04 % Allowed : 6.98 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1525 helix: 1.28 (0.24), residues: 525 sheet: 0.76 (0.28), residues: 395 loop : -2.33 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 206 HIS 0.002 0.001 HIS A 177 PHE 0.010 0.001 PHE E 236 TYR 0.014 0.001 TYR C 245 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.390 Fit side-chains REVERT: A 21 ASN cc_start: 0.8036 (t0) cc_final: 0.7830 (t0) REVERT: A 54 LYS cc_start: 0.8716 (mttt) cc_final: 0.8432 (mtmt) REVERT: A 65 ARG cc_start: 0.7569 (mtp-110) cc_final: 0.7354 (mtp-110) REVERT: A 86 ASP cc_start: 0.7941 (t0) cc_final: 0.7456 (t70) REVERT: B 54 LYS cc_start: 0.8440 (mttt) cc_final: 0.8233 (mtmt) REVERT: B 65 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7253 (mtm180) REVERT: B 86 ASP cc_start: 0.7725 (t0) cc_final: 0.7380 (t70) REVERT: C 245 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7336 (t80) REVERT: D 65 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7375 (mtp-110) REVERT: D 86 ASP cc_start: 0.7748 (t0) cc_final: 0.7255 (t70) REVERT: D 174 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.7490 (mtp85) REVERT: D 245 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7241 (t80) REVERT: E 21 ASN cc_start: 0.8292 (t0) cc_final: 0.8036 (t0) REVERT: E 65 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7131 (mtm180) REVERT: E 174 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: E 245 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6584 (t80) outliers start: 28 outliers final: 20 residues processed: 151 average time/residue: 0.2952 time to fit residues: 61.9838 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 182 GLN D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13130 Z= 0.296 Angle : 0.573 5.332 17825 Z= 0.295 Chirality : 0.050 0.202 1960 Planarity : 0.004 0.035 2250 Dihedral : 12.223 89.947 1925 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.84 % Allowed : 7.27 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1525 helix: 1.39 (0.24), residues: 530 sheet: 0.66 (0.28), residues: 395 loop : -2.27 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.003 0.001 HIS E 177 PHE 0.012 0.002 PHE A 121 TYR 0.017 0.002 TYR D 245 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.895 Fit side-chains REVERT: A 21 ASN cc_start: 0.8124 (t0) cc_final: 0.7829 (t0) REVERT: A 34 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (mmtp) REVERT: A 54 LYS cc_start: 0.8778 (mttt) cc_final: 0.8467 (mtmt) REVERT: A 65 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7402 (mtp-110) REVERT: A 86 ASP cc_start: 0.7867 (t0) cc_final: 0.7311 (t70) REVERT: B 54 LYS cc_start: 0.8402 (mttt) cc_final: 0.8116 (mtmt) REVERT: B 65 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7286 (mtm180) REVERT: B 86 ASP cc_start: 0.7704 (t0) cc_final: 0.7381 (t70) REVERT: C 245 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7205 (t80) REVERT: D 65 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7438 (mtp-110) REVERT: D 86 ASP cc_start: 0.7829 (t0) cc_final: 0.7425 (t70) REVERT: D 174 ARG cc_start: 0.7735 (ttt-90) cc_final: 0.7482 (mtp85) REVERT: D 245 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7242 (t80) REVERT: E 21 ASN cc_start: 0.8389 (t0) cc_final: 0.8173 (t0) REVERT: E 65 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7245 (mtm180) REVERT: E 245 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6361 (t80) outliers start: 39 outliers final: 28 residues processed: 151 average time/residue: 0.3370 time to fit residues: 71.5741 Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13130 Z= 0.273 Angle : 0.550 5.085 17825 Z= 0.283 Chirality : 0.049 0.207 1960 Planarity : 0.004 0.034 2250 Dihedral : 11.611 88.633 1925 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.69 % Allowed : 9.24 % Favored : 88.07 % 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: -0.16 (0.23), residues: 1525 helix: 1.60 (0.23), residues: 525 sheet: 0.67 (0.28), residues: 395 loop : -2.31 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 206 HIS 0.003 0.001 HIS E 177 PHE 0.016 0.001 PHE C 236 TYR 0.018 0.002 TYR D 245 ARG 0.004 0.000 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8648 (mmtp) REVERT: A 54 LYS cc_start: 0.8764 (mttt) cc_final: 0.8463 (mtmt) REVERT: A 65 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.7359 (mtp-110) REVERT: A 86 ASP cc_start: 0.7865 (t0) cc_final: 0.7311 (t70) REVERT: A 187 GLU cc_start: 0.7331 (tt0) cc_final: 0.7107 (tt0) REVERT: B 65 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7341 (mtm180) REVERT: B 86 ASP cc_start: 0.7777 (t0) cc_final: 0.7418 (t70) REVERT: C 245 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7215 (t80) REVERT: D 65 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7440 (mtp-110) REVERT: D 86 ASP cc_start: 0.7803 (t0) cc_final: 0.7401 (t70) REVERT: D 174 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7493 (mtp85) REVERT: D 245 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7301 (t80) REVERT: E 21 ASN cc_start: 0.8351 (t0) cc_final: 0.8132 (t0) REVERT: E 65 ARG cc_start: 0.7565 (mtp-110) cc_final: 0.7229 (mtm180) REVERT: E 245 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.6388 (t80) outliers start: 37 outliers final: 28 residues processed: 151 average time/residue: 0.3058 time to fit residues: 65.5961 Evaluate side-chains 151 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 0.0170 chunk 139 optimal weight: 0.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 182 GLN D 124 GLN D 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13130 Z= 0.160 Angle : 0.496 5.071 17825 Z= 0.253 Chirality : 0.047 0.214 1960 Planarity : 0.003 0.033 2250 Dihedral : 10.697 79.357 1925 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.55 % Allowed : 9.96 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1525 helix: 1.74 (0.23), residues: 525 sheet: 0.80 (0.28), residues: 395 loop : -2.31 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.002 0.000 HIS E 177 PHE 0.011 0.001 PHE D 236 TYR 0.013 0.001 TYR B 245 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.409 Fit side-chains REVERT: A 54 LYS cc_start: 0.8645 (mttt) cc_final: 0.8376 (mtmt) REVERT: A 86 ASP cc_start: 0.7840 (t0) cc_final: 0.7313 (t70) REVERT: A 137 ASN cc_start: 0.8402 (p0) cc_final: 0.8079 (p0) REVERT: A 187 GLU cc_start: 0.7295 (tt0) cc_final: 0.7063 (tt0) REVERT: B 65 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7341 (mtm180) REVERT: B 86 ASP cc_start: 0.7731 (t0) cc_final: 0.7408 (t70) REVERT: C 86 ASP cc_start: 0.7804 (t0) cc_final: 0.7507 (t70) REVERT: C 174 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7373 (ttm-80) REVERT: C 245 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7186 (t80) REVERT: D 65 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.7402 (mtp-110) REVERT: D 86 ASP cc_start: 0.7785 (t0) cc_final: 0.7375 (t70) REVERT: D 162 ILE cc_start: 0.8587 (mm) cc_final: 0.8355 (mm) REVERT: D 174 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7470 (mtp85) REVERT: D 245 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7292 (t80) REVERT: D 263 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: E 21 ASN cc_start: 0.8296 (t0) cc_final: 0.8028 (t0) REVERT: E 65 ARG cc_start: 0.7488 (mtp-110) cc_final: 0.7161 (mtm180) REVERT: E 174 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7418 (mtp85) REVERT: E 245 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6440 (t80) REVERT: E 263 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (m-30) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 0.2979 time to fit residues: 63.5901 Evaluate side-chains 146 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13130 Z= 0.362 Angle : 0.593 5.711 17825 Z= 0.305 Chirality : 0.051 0.214 1960 Planarity : 0.004 0.038 2250 Dihedral : 11.095 89.185 1925 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.13 % Allowed : 9.75 % Favored : 87.13 % 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: -0.10 (0.22), residues: 1525 helix: 1.70 (0.23), residues: 530 sheet: 0.95 (0.30), residues: 345 loop : -2.28 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.003 0.001 HIS E 177 PHE 0.016 0.002 PHE E 236 TYR 0.020 0.002 TYR D 245 ARG 0.006 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8757 (mttt) cc_final: 0.8454 (mtmt) REVERT: A 145 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9086 (tt) REVERT: B 65 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7392 (mtm180) REVERT: B 86 ASP cc_start: 0.7752 (t0) cc_final: 0.7385 (t70) REVERT: C 245 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7203 (t80) REVERT: D 65 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7520 (mtp-110) REVERT: D 86 ASP cc_start: 0.7800 (t0) cc_final: 0.7356 (t70) REVERT: D 174 ARG cc_start: 0.7715 (ttt-90) cc_final: 0.7501 (mtp85) REVERT: D 245 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7246 (t80) REVERT: D 263 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: E 21 ASN cc_start: 0.8419 (t0) cc_final: 0.8188 (t0) REVERT: E 65 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.7237 (mtm180) REVERT: E 174 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7390 (mtp85) REVERT: E 245 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6323 (t80) REVERT: E 263 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7474 (m-30) outliers start: 43 outliers final: 32 residues processed: 148 average time/residue: 0.2945 time to fit residues: 61.2075 Evaluate side-chains 158 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13130 Z= 0.151 Angle : 0.494 5.311 17825 Z= 0.251 Chirality : 0.047 0.222 1960 Planarity : 0.003 0.031 2250 Dihedral : 10.130 75.253 1925 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.91 % Allowed : 10.11 % Favored : 86.98 % 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: 0.02 (0.23), residues: 1525 helix: 1.86 (0.23), residues: 525 sheet: 0.81 (0.28), residues: 395 loop : -2.36 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.002 0.000 HIS D 177 PHE 0.011 0.001 PHE D 236 TYR 0.013 0.001 TYR B 245 ARG 0.007 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.542 Fit side-chains REVERT: A 54 LYS cc_start: 0.8619 (mttt) cc_final: 0.8374 (mtmt) REVERT: A 86 ASP cc_start: 0.7910 (t0) cc_final: 0.7360 (t70) REVERT: A 145 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 245 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 65 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7340 (mtm180) REVERT: B 86 ASP cc_start: 0.7706 (t0) cc_final: 0.7362 (t70) REVERT: C 86 ASP cc_start: 0.7812 (t0) cc_final: 0.7507 (t70) REVERT: C 245 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7089 (t80) REVERT: D 30 GLU cc_start: 0.6607 (tp30) cc_final: 0.5338 (tt0) REVERT: D 65 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7444 (mtp-110) REVERT: D 86 ASP cc_start: 0.7809 (t0) cc_final: 0.7402 (t70) REVERT: D 162 ILE cc_start: 0.8558 (mm) cc_final: 0.8321 (mm) REVERT: D 174 ARG cc_start: 0.7710 (ttt-90) cc_final: 0.7484 (mtp85) REVERT: D 245 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7234 (t80) REVERT: D 263 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: E 21 ASN cc_start: 0.8275 (t0) cc_final: 0.8022 (t0) REVERT: E 65 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7131 (mtm180) REVERT: E 174 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7419 (mtp85) REVERT: E 245 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6551 (t80) REVERT: E 263 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: E 265 MET cc_start: 0.8096 (mtp) cc_final: 0.7792 (mtp) outliers start: 40 outliers final: 25 residues processed: 156 average time/residue: 0.2967 time to fit residues: 64.9553 Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13130 Z= 0.258 Angle : 0.543 5.236 17825 Z= 0.278 Chirality : 0.049 0.217 1960 Planarity : 0.004 0.036 2250 Dihedral : 10.262 78.843 1925 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.76 % Allowed : 10.40 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1525 helix: 1.92 (0.23), residues: 525 sheet: 1.10 (0.30), residues: 345 loop : -2.31 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.002 0.001 HIS E 177 PHE 0.013 0.001 PHE E 236 TYR 0.019 0.001 TYR D 245 ARG 0.006 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.566 Fit side-chains REVERT: A 30 GLU cc_start: 0.6723 (tp30) cc_final: 0.6167 (tp30) REVERT: A 54 LYS cc_start: 0.8693 (mttt) cc_final: 0.8406 (mtmt) REVERT: A 145 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (tt) REVERT: B 65 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7368 (mtm180) REVERT: B 86 ASP cc_start: 0.7747 (t0) cc_final: 0.7374 (t70) REVERT: C 245 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7254 (t80) REVERT: D 30 GLU cc_start: 0.6569 (tp30) cc_final: 0.5563 (tp30) REVERT: D 65 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7470 (mtp-110) REVERT: D 86 ASP cc_start: 0.7776 (t0) cc_final: 0.7378 (t70) REVERT: D 162 ILE cc_start: 0.8688 (mm) cc_final: 0.8394 (mm) REVERT: D 245 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7293 (t80) REVERT: D 263 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: E 21 ASN cc_start: 0.8315 (t0) cc_final: 0.8098 (t0) REVERT: E 65 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7168 (mtm180) REVERT: E 174 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7399 (mtp85) REVERT: E 245 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6458 (t80) REVERT: E 263 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: E 265 MET cc_start: 0.8150 (mtp) cc_final: 0.7845 (mtp) outliers start: 38 outliers final: 30 residues processed: 149 average time/residue: 0.2975 time to fit residues: 62.7940 Evaluate side-chains 157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13130 Z= 0.248 Angle : 0.540 5.335 17825 Z= 0.276 Chirality : 0.049 0.221 1960 Planarity : 0.004 0.034 2250 Dihedral : 10.116 78.516 1925 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.76 % Allowed : 10.47 % Favored : 86.76 % 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: 0.02 (0.23), residues: 1525 helix: 2.00 (0.23), residues: 520 sheet: 1.08 (0.30), residues: 345 loop : -2.38 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 206 HIS 0.003 0.001 HIS E 177 PHE 0.016 0.001 PHE D 236 TYR 0.017 0.001 TYR D 245 ARG 0.009 0.000 ARG A 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.413 Fit side-chains REVERT: A 54 LYS cc_start: 0.8695 (mttt) cc_final: 0.8399 (mtmt) REVERT: A 145 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 65 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7376 (mtm180) REVERT: B 86 ASP cc_start: 0.7758 (t0) cc_final: 0.7397 (t70) REVERT: C 86 ASP cc_start: 0.7802 (t0) cc_final: 0.7493 (t70) REVERT: C 245 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7411 (t80) REVERT: D 30 GLU cc_start: 0.6566 (tp30) cc_final: 0.5574 (tp30) REVERT: D 65 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7467 (mtp-110) REVERT: D 86 ASP cc_start: 0.7783 (t0) cc_final: 0.7381 (t70) REVERT: D 162 ILE cc_start: 0.8643 (mm) cc_final: 0.8393 (mm) REVERT: D 174 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7514 (mtp85) REVERT: D 245 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7277 (t80) REVERT: D 263 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: E 21 ASN cc_start: 0.8400 (t0) cc_final: 0.8085 (t0) REVERT: E 65 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.7150 (mtm180) REVERT: E 174 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7399 (mtp85) REVERT: E 245 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6436 (t80) REVERT: E 263 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7242 (m-30) outliers start: 38 outliers final: 29 residues processed: 148 average time/residue: 0.2939 time to fit residues: 60.9344 Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.0570 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116381 restraints weight = 13158.165| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.49 r_work: 0.3028 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13130 Z= 0.139 Angle : 0.486 5.453 17825 Z= 0.247 Chirality : 0.047 0.223 1960 Planarity : 0.003 0.033 2250 Dihedral : 9.527 67.666 1925 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.69 % Allowed : 10.47 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1525 helix: 2.04 (0.23), residues: 520 sheet: 0.72 (0.26), residues: 460 loop : -2.49 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 206 HIS 0.002 0.000 HIS C 177 PHE 0.011 0.001 PHE D 236 TYR 0.013 0.001 TYR B 245 ARG 0.009 0.000 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.43 seconds wall clock time: 49 minutes 56.46 seconds (2996.46 seconds total)