Starting phenix.real_space_refine on Mon Mar 18 01:32:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/03_2024/6b46_7050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/03_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_7050/03_2024/6b46_7050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/03_2024/6b46_7050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/03_2024/6b46_7050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b46_7050/03_2024/6b46_7050.pdb" } 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 Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 42": "NH1" <-> "NH2" Residue "I ARG 64": "NH1" <-> "NH2" Residue "J ARG 42": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.68, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 3.1 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: 4.84 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: 5.29 Time building geometry restraints manager: 7.31 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: 96.90 - 104.35: 417 104.35 - 111.79: 8549 111.79 - 119.24: 6623 119.24 - 126.68: 9727 126.68 - 134.13: 377 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 2.440 nonbonded pdb=" O SER C 36 " pdb=" NZ LYS C 92 " model vdw 2.309 2.520 nonbonded pdb=" NZ LYS F 259 " pdb=" OP1 U M 22 " model vdw 2.312 2.520 nonbonded pdb=" OD1 ASP C 22 " pdb=" OG SER C 257 " model vdw 2.330 2.440 nonbonded pdb=" OG SER H 287 " pdb=" O LYS H 293 " model vdw 2.340 2.440 ... (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 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 4.220 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 50.760 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.320 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 270 time to evaluate : 2.159 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: 0.4192 time to fit residues: 155.5335 Evaluate side-chains 145 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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: 3.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 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: 5.7990 ------------------------------------------------------------------------------- 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 D 223 GLN E 72 GLN E 208 HIS E 291 GLN F 241 GLN F 291 GLN G 129 GLN H 223 GLN H 241 GLN H 329 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 18791 Z= 0.356 Angle : 0.664 7.970 25693 Z= 0.358 Chirality : 0.044 0.395 2819 Planarity : 0.005 0.064 3213 Dihedral : 15.798 149.118 3459 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.33 % Allowed : 5.91 % Favored : 92.76 % 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: -2.75 (0.16), residues: 2286 helix: -0.57 (0.19), residues: 655 sheet: -0.89 (0.26), residues: 413 loop : -3.01 (0.14), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 311 HIS 0.010 0.002 HIS E 324 PHE 0.021 0.002 PHE J 44 TYR 0.020 0.002 TYR E 305 ARG 0.007 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 176 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.806 Fit side-chains revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: C 259 LYS cc_start: 0.8169 (tttt) cc_final: 0.7622 (tptt) REVERT: D 45 ARG cc_start: 0.7562 (mtm110) cc_final: 0.7301 (mtm-85) REVERT: E 22 ASP cc_start: 0.8248 (m-30) cc_final: 0.7923 (m-30) REVERT: G 60 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8342 (pttt) REVERT: G 114 TYR cc_start: 0.7578 (t80) cc_final: 0.7335 (t80) REVERT: H 34 ASP cc_start: 0.7067 (m-30) cc_final: 0.6711 (t0) REVERT: H 321 GLU cc_start: 0.7134 (mp0) cc_final: 0.6483 (mt-10) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 0.3637 time to fit residues: 86.8325 Evaluate side-chains 148 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 SER 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 F residue 283 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 80 ASP 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 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 0.0970 chunk 71 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 151 ASN C 297 GLN D 164 HIS D 223 GLN F 241 GLN H 151 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18791 Z= 0.307 Angle : 0.610 7.861 25693 Z= 0.329 Chirality : 0.043 0.325 2819 Planarity : 0.005 0.062 3213 Dihedral : 15.661 150.151 3459 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.11 % Allowed : 7.48 % Favored : 90.40 % 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: -2.09 (0.17), residues: 2286 helix: 0.31 (0.20), residues: 655 sheet: -0.59 (0.27), residues: 404 loop : -2.77 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 311 HIS 0.008 0.002 HIS E 324 PHE 0.026 0.002 PHE J 44 TYR 0.018 0.002 TYR E 305 ARG 0.006 0.001 ARG E 146 *********************** 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 193 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: C 230 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6991 (mm-30) REVERT: C 259 LYS cc_start: 0.8155 (tttt) cc_final: 0.7834 (tttp) REVERT: D 45 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7156 (mtm-85) REVERT: E 22 ASP cc_start: 0.8218 (m-30) cc_final: 0.7954 (m-30) REVERT: F 32 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: F 228 SER cc_start: 0.8702 (p) cc_final: 0.8479 (m) REVERT: G 60 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8213 (pttt) REVERT: H 34 ASP cc_start: 0.6954 (m-30) cc_final: 0.6572 (t0) REVERT: H 321 GLU cc_start: 0.7008 (mp0) cc_final: 0.6420 (mt-10) REVERT: I 39 VAL cc_start: 0.8136 (m) cc_final: 0.7861 (p) outliers start: 35 outliers final: 22 residues processed: 178 average time/residue: 0.3391 time to fit residues: 88.7336 Evaluate side-chains 161 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP 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 170 VAL Chi-restraints excluded: chain D residue 183 LEU 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 F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 206 SER 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 H residue 221 ASP Chi-restraints excluded: chain J residue 8 SER 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: 9.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 211 optimal weight: 40.0000 chunk 224 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN G 140 HIS H 37 GLN H 223 GLN ** H 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18791 Z= 0.431 Angle : 0.697 8.535 25693 Z= 0.372 Chirality : 0.046 0.351 2819 Planarity : 0.005 0.060 3213 Dihedral : 15.764 152.108 3459 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.84 % Allowed : 8.93 % Favored : 88.23 % 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: -1.95 (0.17), residues: 2286 helix: 0.40 (0.20), residues: 660 sheet: -0.36 (0.27), residues: 416 loop : -2.76 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 311 HIS 0.008 0.002 HIS C 256 PHE 0.023 0.002 PHE J 44 TYR 0.021 0.003 TYR E 305 ARG 0.010 0.001 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 4 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 179 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 2.014 Fit side-chains revert: symmetry clash REVERT: C 25 MET cc_start: 0.8413 (mtp) cc_final: 0.8070 (mtt) REVERT: C 83 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7350 (t0) REVERT: C 230 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6966 (mm-30) REVERT: C 259 LYS cc_start: 0.8217 (tttt) cc_final: 0.7691 (tptt) REVERT: D 45 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7195 (mtm-85) REVERT: E 22 ASP cc_start: 0.8245 (m-30) cc_final: 0.7997 (m-30) REVERT: F 32 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: F 228 SER cc_start: 0.8799 (p) cc_final: 0.8545 (m) REVERT: H 34 ASP cc_start: 0.7005 (m-30) cc_final: 0.6376 (t0) REVERT: H 224 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6149 (tp30) REVERT: H 321 GLU cc_start: 0.7072 (mp0) cc_final: 0.6735 (mt-10) REVERT: I 71 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7394 (tm-30) REVERT: J 71 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6878 (tm-30) outliers start: 47 outliers final: 32 residues processed: 165 average time/residue: 0.3293 time to fit residues: 81.0789 Evaluate side-chains 158 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP 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 19 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 3 optimal weight: 0.0470 chunk 166 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 191 optimal weight: 40.0000 chunk 155 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN H 37 GLN H 223 GLN H 323 GLN I 49 GLN J 16 ASN ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18791 Z= 0.138 Angle : 0.505 8.655 25693 Z= 0.274 Chirality : 0.039 0.305 2819 Planarity : 0.003 0.050 3213 Dihedral : 15.404 151.943 3459 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.11 % Allowed : 10.62 % Favored : 87.27 % 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: -1.45 (0.17), residues: 2286 helix: 1.06 (0.21), residues: 658 sheet: -0.24 (0.27), residues: 414 loop : -2.52 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 174 HIS 0.006 0.001 HIS G 324 PHE 0.026 0.001 PHE J 44 TYR 0.013 0.002 TYR G 114 ARG 0.003 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 5 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 191 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: C 25 MET cc_start: 0.8378 (mtp) cc_final: 0.8046 (mtt) REVERT: C 83 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7168 (t0) REVERT: C 230 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6854 (mm-30) REVERT: D 45 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: E 22 ASP cc_start: 0.8079 (m-30) cc_final: 0.7813 (m-30) REVERT: F 32 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: H 34 ASP cc_start: 0.7155 (m-30) cc_final: 0.6493 (t0) REVERT: H 323 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5663 (mp-120) REVERT: H 332 ARG cc_start: 0.5354 (OUTLIER) cc_final: 0.4474 (tmt-80) REVERT: I 71 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7483 (tm-30) REVERT: J 71 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6889 (tm-30) REVERT: J 72 ILE cc_start: 0.7717 (mt) cc_final: 0.7423 (mt) outliers start: 35 outliers final: 20 residues processed: 180 average time/residue: 0.3507 time to fit residues: 92.0494 Evaluate side-chains 155 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 169 GLU 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 159 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 206 SER 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 H residue 203 LEU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 323 GLN Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 224 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN H 37 GLN H 208 HIS H 223 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18791 Z= 0.162 Angle : 0.508 8.976 25693 Z= 0.271 Chirality : 0.039 0.293 2819 Planarity : 0.003 0.056 3213 Dihedral : 15.352 152.782 3459 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.11 % Allowed : 11.83 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2286 helix: 1.32 (0.21), residues: 656 sheet: -0.14 (0.27), residues: 419 loop : -2.40 (0.16), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 53 HIS 0.010 0.001 HIS H 324 PHE 0.009 0.001 PHE C 147 TYR 0.013 0.001 TYR G 285 ARG 0.003 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 6 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 173 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: C 25 MET cc_start: 0.8397 (mtp) cc_final: 0.8060 (mtt) REVERT: C 83 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7166 (t0) REVERT: C 230 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6816 (mm-30) REVERT: D 45 ARG cc_start: 0.7415 (mtm110) cc_final: 0.7125 (mtm-85) REVERT: D 67 LEU cc_start: 0.6040 (tt) cc_final: 0.5108 (mt) REVERT: E 22 ASP cc_start: 0.8065 (m-30) cc_final: 0.7797 (m-30) REVERT: F 32 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: G 114 TYR cc_start: 0.7303 (t80) cc_final: 0.6963 (t80) REVERT: H 34 ASP cc_start: 0.7138 (m-30) cc_final: 0.6459 (t0) REVERT: H 83 ASN cc_start: 0.7799 (m-40) cc_final: 0.6801 (m-40) REVERT: H 224 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: I 39 VAL cc_start: 0.8190 (m) cc_final: 0.7858 (p) REVERT: I 71 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7483 (tm-30) REVERT: J 71 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6719 (tm-30) REVERT: J 72 ILE cc_start: 0.7669 (mt) cc_final: 0.7455 (mt) outliers start: 35 outliers final: 23 residues processed: 160 average time/residue: 0.3366 time to fit residues: 79.9694 Evaluate side-chains 157 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 206 SER 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 H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN ** H 241 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18791 Z= 0.231 Angle : 0.542 8.482 25693 Z= 0.288 Chirality : 0.040 0.293 2819 Planarity : 0.004 0.055 3213 Dihedral : 15.369 153.321 3459 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.35 % Allowed : 11.59 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2286 helix: 1.33 (0.21), residues: 655 sheet: -0.17 (0.28), residues: 407 loop : -2.37 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 311 HIS 0.004 0.001 HIS G 324 PHE 0.010 0.001 PHE C 147 TYR 0.014 0.002 TYR G 285 ARG 0.004 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 7 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 168 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: C 25 MET cc_start: 0.8445 (mtp) cc_final: 0.8105 (mtt) REVERT: C 83 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7083 (t0) REVERT: C 230 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6849 (mm-30) REVERT: C 259 LYS cc_start: 0.8141 (tttt) cc_final: 0.7801 (tttp) REVERT: D 45 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7122 (mtm-85) REVERT: E 22 ASP cc_start: 0.8108 (m-30) cc_final: 0.7844 (m-30) REVERT: F 32 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: G 140 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: H 34 ASP cc_start: 0.7137 (m-30) cc_final: 0.6415 (t0) REVERT: H 83 ASN cc_start: 0.7854 (m-40) cc_final: 0.6890 (m-40) REVERT: H 224 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.5983 (tp30) REVERT: I 25 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7423 (pttt) REVERT: I 71 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7472 (tm-30) REVERT: J 71 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6701 (tm-30) REVERT: J 72 ILE cc_start: 0.7676 (mt) cc_final: 0.7458 (mt) outliers start: 39 outliers final: 30 residues processed: 150 average time/residue: 0.3408 time to fit residues: 75.0812 Evaluate side-chains 164 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 67 optimal weight: 0.0570 chunk 43 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 214 optimal weight: 50.0000 overall best weight: 4.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN ** H 241 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18791 Z= 0.290 Angle : 0.582 8.182 25693 Z= 0.309 Chirality : 0.042 0.306 2819 Planarity : 0.004 0.053 3213 Dihedral : 15.457 153.629 3459 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.08 % Allowed : 11.04 % Favored : 85.88 % 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: -1.27 (0.17), residues: 2286 helix: 1.23 (0.21), residues: 656 sheet: -0.05 (0.28), residues: 399 loop : -2.43 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 311 HIS 0.005 0.001 HIS G 324 PHE 0.011 0.001 PHE C 147 TYR 0.024 0.002 TYR G 247 ARG 0.005 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 8 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 182 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 131 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: C 25 MET cc_start: 0.8485 (mtp) cc_final: 0.8152 (mtt) REVERT: C 83 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.7118 (t0) REVERT: C 230 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6899 (mm-30) REVERT: C 259 LYS cc_start: 0.8166 (tttt) cc_final: 0.7839 (tttp) REVERT: D 45 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7155 (mtm-85) REVERT: E 22 ASP cc_start: 0.8175 (m-30) cc_final: 0.7921 (m-30) REVERT: E 37 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: E 119 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7403 (mm) REVERT: F 32 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: G 140 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7588 (t-90) REVERT: H 224 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6047 (tp30) REVERT: I 71 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7358 (tm-30) REVERT: J 71 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6721 (tm-30) REVERT: J 72 ILE cc_start: 0.7626 (mt) cc_final: 0.7414 (mt) outliers start: 51 outliers final: 35 residues processed: 163 average time/residue: 0.3414 time to fit residues: 83.0103 Evaluate side-chains 168 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP 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 19 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 50.0000 chunk 214 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 0.0670 chunk 197 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN ** H 241 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18791 Z= 0.254 Angle : 0.559 8.213 25693 Z= 0.298 Chirality : 0.041 0.304 2819 Planarity : 0.004 0.053 3213 Dihedral : 15.425 153.596 3459 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.78 % Allowed : 11.41 % Favored : 85.82 % 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: -1.20 (0.17), residues: 2286 helix: 1.32 (0.21), residues: 654 sheet: -0.04 (0.27), residues: 413 loop : -2.41 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 30 HIS 0.005 0.001 HIS G 324 PHE 0.022 0.001 PHE J 44 TYR 0.020 0.002 TYR G 247 ARG 0.004 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 9 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 172 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: C 25 MET cc_start: 0.8494 (mtp) cc_final: 0.8176 (mtt) REVERT: C 83 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7087 (t0) REVERT: C 230 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6980 (mm-30) REVERT: D 45 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7162 (mtm-85) REVERT: E 22 ASP cc_start: 0.8153 (m-30) cc_final: 0.7890 (m-30) REVERT: E 37 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: E 119 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7402 (mm) REVERT: F 32 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: G 140 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: H 224 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6026 (tp30) REVERT: I 71 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7423 (tm-30) REVERT: J 71 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6947 (tm-30) REVERT: J 72 ILE cc_start: 0.7593 (mt) cc_final: 0.7297 (mt) outliers start: 46 outliers final: 35 residues processed: 154 average time/residue: 0.3328 time to fit residues: 75.7807 Evaluate side-chains 169 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 77 GLN 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 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 231 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 146 optimal weight: 0.0980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN ** H 241 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18791 Z= 0.187 Angle : 0.525 8.709 25693 Z= 0.281 Chirality : 0.040 0.293 2819 Planarity : 0.003 0.052 3213 Dihedral : 15.341 153.544 3459 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.35 % Allowed : 12.13 % Favored : 85.52 % 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: -1.07 (0.18), residues: 2286 helix: 1.50 (0.21), residues: 655 sheet: -0.02 (0.27), residues: 415 loop : -2.35 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 53 HIS 0.004 0.001 HIS G 324 PHE 0.010 0.001 PHE J 44 TYR 0.073 0.002 TYR C 295 ARG 0.004 0.000 ARG C 296 ********************** REFINEMENT MACRO_CYCLE 10 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 167 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: C 25 MET cc_start: 0.8455 (mtp) cc_final: 0.8141 (mtt) REVERT: C 83 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7070 (t0) REVERT: C 230 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6893 (mm-30) REVERT: D 45 ARG cc_start: 0.7405 (mtm110) cc_final: 0.7152 (mtm-85) REVERT: E 22 ASP cc_start: 0.8106 (m-30) cc_final: 0.7846 (m-30) REVERT: E 37 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: E 119 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (mm) REVERT: F 32 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: G 140 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7554 (t-90) REVERT: H 224 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.5990 (tp30) REVERT: I 39 VAL cc_start: 0.8190 (m) cc_final: 0.7822 (p) REVERT: I 71 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7420 (tm-30) REVERT: J 72 ILE cc_start: 0.7595 (mt) cc_final: 0.7298 (mt) outliers start: 39 outliers final: 28 residues processed: 153 average time/residue: 0.3668 time to fit residues: 84.6241 Evaluate side-chains 161 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ASP 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 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN F 241 GLN G 164 HIS ** H 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111678 restraints weight = 30871.111| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.66 r_work: 0.3272 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18791 Z= 0.409 Angle : 0.660 8.643 25693 Z= 0.350 Chirality : 0.045 0.321 2819 Planarity : 0.005 0.052 3213 Dihedral : 15.596 154.224 3459 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.66 % Allowed : 11.89 % Favored : 85.46 % 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: -1.33 (0.17), residues: 2286 helix: 1.12 (0.21), residues: 654 sheet: 0.01 (0.28), residues: 397 loop : -2.46 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 311 HIS 0.007 0.002 HIS C 256 PHE 0.025 0.002 PHE J 44 TYR 0.061 0.003 TYR C 295 ARG 0.007 0.001 ARG F 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.17 seconds wall clock time: 69 minutes 9.86 seconds (4149.86 seconds total)