Starting phenix.real_space_refine on Tue Nov 19 10:46:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/11_2024/6b46_7050.cif" } resolution = 3.1 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= 0.056 sd= 1.082 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 1240 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 59 5.49 5 S 18 5.16 5 C 11200 2.51 5 N 3374 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18344 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "J" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 10.83, per 1000 atoms: 0.59 Number of scatterers: 18344 At special positions: 0 Unit cell: (127.937, 122.985, 151.048, 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 18 16.00 P 59 15.00 O 3693 8.00 N 3374 7.00 C 11200 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: 4.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3932 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 38 sheets defined 29.0% alpha, 20.6% beta 1 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.738A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 removed outlier: 3.863A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.633A pdb=" N GLY C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.595A pdb=" N ALA D 35 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 32 through 36' Processing helix chain 'D' and resid 65 through 73 removed outlier: 5.453A pdb=" N ILE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.511A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.766A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.502A pdb=" N GLN E 129 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 205 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.832A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.578A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.700A pdb=" N GLN F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 205 Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.679A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 312 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.503A pdb=" N LEU G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.689A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 292 Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 189 through 204 removed outlier: 3.740A pdb=" N SER H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 304 through 313 removed outlier: 3.638A pdb=" N LEU H 313 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.713A pdb=" N GLN H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 Processing helix chain 'I' and resid 61 through 73 Processing helix chain 'J' and resid 46 through 55 Processing helix chain 'J' and resid 61 through 73 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.645A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.503A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 210 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 172 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.826A pdb=" N ARG C 94 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 23 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 255 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 252 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA5, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.255A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.515A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.217A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.518A pdb=" N ILE D 255 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 252 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 51 removed outlier: 3.925A pdb=" N GLY D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 75 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.675A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.355A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.843A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 50 removed outlier: 3.572A pdb=" N VAL E 81 " --> pdb=" O ARG E 45 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AB8, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AB9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.545A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.507A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 162 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.691A pdb=" N VAL F 49 " --> pdb=" O GLN F 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.979A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.550A pdb=" N ARG G 94 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.193A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 50 Processing sheet with id=AC9, first strand: chain 'G' and resid 229 through 230 removed outlier: 4.711A pdb=" N THR G 245 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 248 through 249 removed outlier: 3.571A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD3, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'H' and resid 12 through 14 removed outlier: 4.073A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE H 336 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.484A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 170 through 173 removed outlier: 6.718A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 23 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 252 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.818A pdb=" N VAL H 81 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 47 " --> pdb=" O VAL H 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.870A pdb=" N ASP H 268 " --> pdb=" O ILE H 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 2 through 6 removed outlier: 3.700A pdb=" N LYS I 2 " --> pdb=" O GLU I 21 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL I 19 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR I 6 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE I 17 " --> pdb=" O TYR I 6 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY I 40 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN I 32 " --> pdb=" O SER I 38 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER I 38 " --> pdb=" O ASN I 32 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 2 through 6 removed outlier: 3.700A pdb=" N LYS J 2 " --> pdb=" O GLU J 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL J 19 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR J 6 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE J 17 " --> pdb=" O TYR J 6 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY J 40 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN J 32 " --> pdb=" O SER J 38 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER J 38 " --> pdb=" O ASN J 32 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 5 through 7 741 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4999 1.33 - 1.45: 3492 1.45 - 1.57: 10152 1.57 - 1.68: 118 1.68 - 1.80: 30 Bond restraints: 18791 Sorted by residual: bond pdb=" C PHE L 158 " pdb=" N ILE L 159 " ideal model delta sigma weight residual 1.332 1.312 0.020 5.60e-03 3.19e+04 1.21e+01 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.96e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.24e+00 bond pdb=" CB TRP G 270 " pdb=" CG TRP G 270 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.21e+00 bond pdb=" CG1 ILE F 267 " pdb=" CD1 ILE F 267 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 ... (remaining 18786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 25152 2.54 - 5.09: 479 5.09 - 7.63: 47 7.63 - 10.17: 13 10.17 - 12.72: 2 Bond angle restraints: 25693 Sorted by residual: angle pdb=" C ARG F 296 " pdb=" N GLN F 297 " pdb=" CA GLN F 297 " ideal model delta sigma weight residual 120.49 129.77 -9.28 1.42e+00 4.96e-01 4.27e+01 angle pdb=" C ARG H 250 " pdb=" N ASP H 251 " pdb=" CA ASP H 251 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C LYS G 58 " pdb=" N THR G 59 " pdb=" CA THR G 59 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C LYS E 238 " pdb=" N LYS E 239 " pdb=" CA LYS E 239 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CA GLN D 241 " pdb=" CB GLN D 241 " pdb=" CG GLN D 241 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.50e+01 ... (remaining 25688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 10763 30.12 - 60.23: 266 60.23 - 90.35: 77 90.35 - 120.47: 2 120.47 - 150.59: 2 Dihedral angle restraints: 11110 sinusoidal: 4819 harmonic: 6291 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 49.41 150.59 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 69.28 130.72 1 1.50e+01 4.44e-03 7.05e+01 dihedral pdb=" CA TRP C 270 " pdb=" C TRP C 270 " pdb=" N TYR C 271 " pdb=" CA TYR C 271 " ideal model delta harmonic sigma weight residual 180.00 148.86 31.14 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 11107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2718 0.115 - 0.231: 93 0.231 - 0.346: 7 0.346 - 0.462: 0 0.462 - 0.577: 1 Chirality restraints: 2819 Sorted by residual: chirality pdb=" C1' C M 1 " pdb=" O4' C M 1 " pdb=" C2' C M 1 " pdb=" N1 C M 1 " both_signs ideal model delta sigma weight residual False 2.46 1.88 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CB ILE D 267 " pdb=" CA ILE D 267 " pdb=" CG1 ILE D 267 " pdb=" CG2 ILE D 267 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' C M 1 " pdb=" C4' C M 1 " pdb=" O3' C M 1 " pdb=" C2' C M 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2816 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " 0.019 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" CG TRP D 311 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A M 12 " -0.035 2.00e-02 2.50e+03 1.67e-02 7.68e+00 pdb=" N9 A M 12 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A M 12 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A M 12 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A M 12 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A M 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A M 12 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A M 12 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 297 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO E 298 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5304 2.82 - 3.34: 15175 3.34 - 3.86: 29758 3.86 - 4.38: 34352 4.38 - 4.90: 58550 Nonbonded interactions: 143139 Sorted by model distance: nonbonded pdb=" OE2 GLU E 283 " pdb=" OG SER E 287 " model vdw 2.296 3.040 nonbonded pdb=" O SER C 36 " pdb=" NZ LYS C 92 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS F 259 " pdb=" OP1 U M 22 " model vdw 2.312 3.120 nonbonded pdb=" OD1 ASP C 22 " pdb=" OG SER C 257 " model vdw 2.330 3.040 nonbonded pdb=" OG SER H 287 " pdb=" O LYS H 293 " model vdw 2.340 3.040 ... (remaining 143134 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 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.350 Find NCS groups from input model: 0.810 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.006 0.067 18791 Z= 0.385 Angle : 0.872 12.715 25693 Z= 0.490 Chirality : 0.054 0.577 2819 Planarity : 0.006 0.063 3213 Dihedral : 14.100 150.587 7178 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.47 % Rotamer: Outliers : 0.18 % Allowed : 1.39 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.14), residues: 2286 helix: -2.42 (0.15), residues: 652 sheet: -1.60 (0.25), residues: 415 loop : -3.20 (0.14), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP D 311 HIS 0.019 0.004 HIS E 324 PHE 0.028 0.003 PHE E 336 TYR 0.035 0.004 TYR F 138 ARG 0.009 0.001 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 270 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 LEU cc_start: 0.7023 (mm) cc_final: 0.6776 (tp) REVERT: C 250 ARG cc_start: 0.6832 (ptt180) cc_final: 0.6500 (ptp-110) REVERT: C 277 LEU cc_start: 0.6566 (mp) cc_final: 0.6342 (mp) REVERT: D 45 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7306 (mtm-85) REVERT: H 34 ASP cc_start: 0.7005 (m-30) cc_final: 0.6656 (t0) REVERT: I 9 THR cc_start: 0.8795 (m) cc_final: 0.8490 (t) outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.4441 time to fit residues: 165.3539 Evaluate side-chains 145 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 129 GLN C 164 HIS D 129 GLN E 208 HIS F 241 GLN F 291 GLN G 129 GLN H 151 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18791 Z= 0.274 Angle : 0.625 7.769 25693 Z= 0.338 Chirality : 0.043 0.387 2819 Planarity : 0.005 0.063 3213 Dihedral : 15.794 148.875 3459 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.33 % Allowed : 5.55 % Favored : 93.12 % 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: -2.73 (0.16), residues: 2286 helix: -0.61 (0.19), residues: 661 sheet: -0.82 (0.26), residues: 400 loop : -2.98 (0.14), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 311 HIS 0.010 0.002 HIS E 324 PHE 0.015 0.002 PHE J 44 TYR 0.018 0.002 TYR C 271 ARG 0.006 0.001 ARG H 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 136 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7695 (mtm-85) REVERT: C 277 LEU cc_start: 0.6368 (mp) cc_final: 0.6140 (mp) REVERT: D 45 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7271 (mtm-85) REVERT: F 228 SER cc_start: 0.8682 (p) cc_final: 0.8413 (m) REVERT: G 60 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (pttt) REVERT: H 34 ASP cc_start: 0.6719 (m-30) cc_final: 0.6415 (t0) REVERT: H 321 GLU cc_start: 0.7103 (mp0) cc_final: 0.6432 (mt-10) REVERT: H 325 TYR cc_start: 0.7268 (t80) cc_final: 0.6842 (t80) REVERT: J 31 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7394 (mt-10) outliers start: 22 outliers final: 13 residues processed: 179 average time/residue: 0.4076 time to fit residues: 106.0440 Evaluate side-chains 156 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN D 164 HIS F 241 GLN ** H 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18791 Z= 0.230 Angle : 0.563 6.997 25693 Z= 0.305 Chirality : 0.041 0.309 2819 Planarity : 0.004 0.060 3213 Dihedral : 15.648 149.861 3459 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.75 % Allowed : 7.00 % Favored : 91.25 % 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: -2.06 (0.17), residues: 2286 helix: 0.30 (0.20), residues: 665 sheet: -0.48 (0.27), residues: 402 loop : -2.78 (0.15), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 311 HIS 0.007 0.001 HIS E 324 PHE 0.024 0.001 PHE J 44 TYR 0.015 0.002 TYR H 114 ARG 0.005 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6947 (mm-30) REVERT: C 277 LEU cc_start: 0.6221 (mp) cc_final: 0.5980 (mp) REVERT: D 45 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7353 (mtm-85) REVERT: F 32 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: G 60 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8221 (pttt) REVERT: H 321 GLU cc_start: 0.7082 (mp0) cc_final: 0.6501 (mt-10) REVERT: J 52 SER cc_start: 0.8635 (p) cc_final: 0.8425 (p) outliers start: 29 outliers final: 19 residues processed: 169 average time/residue: 0.3917 time to fit residues: 97.1482 Evaluate side-chains 157 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 50.0000 chunk 158 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 50.0000 chunk 224 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN H 323 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2535 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: