Starting phenix.real_space_refine on Wed Feb 14 04:50:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv3_32136/02_2024/7vv3_32136_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5531 2.51 5 N 1449 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8633 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Unusual residues: {'CLR': 1} Classifications: {'peptide': 262, 'undetermined': 1} Link IDs: {'PTRANS': 8, 'TRANS': 253, None: 1} Not linked: pdbres="GLN R 288 " pdbres="CLR R 401 " Time building chain proxies: 5.10, per 1000 atoms: 0.59 Number of scatterers: 8633 At special positions: 0 Unit cell: (118.876, 112.564, 104.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1590 8.00 N 1449 7.00 C 5531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 34.7% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.085A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.950A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.638A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'R' and resid 28 through 57 removed outlier: 3.691A pdb=" N ILE R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.657A pdb=" N LEU R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.657A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.508A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.898A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 237 through 243 Processing helix chain 'R' and resid 245 through 250 removed outlier: 3.503A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 258 removed outlier: 4.020A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 279 Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 284 No H-bonds generated for 'chain 'R' and resid 281 through 284' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.514A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.925A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.900A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.672A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.684A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.522A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.618A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.924A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.648A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 213 through 219 removed outlier: 3.515A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG S 168 " --> pdb=" O PRO S 173 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2625 1.34 - 1.47: 2386 1.47 - 1.60: 3724 1.60 - 1.73: 1 1.73 - 1.86: 87 Bond restraints: 8823 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.621 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.36e+01 bond pdb=" C HIS R 261 " pdb=" O HIS R 261 " ideal model delta sigma weight residual 1.244 1.217 0.027 9.80e-03 1.04e+04 7.64e+00 bond pdb=" C ARG S 168 " pdb=" N PRO S 169 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.99e+00 bond pdb=" C ASN R 271 " pdb=" O ASN R 271 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.89e+00 ... (remaining 8818 not shown) Histogram of bond angle deviations from ideal: 95.40 - 105.25: 123 105.25 - 115.10: 5290 115.10 - 124.95: 6358 124.95 - 134.80: 189 134.80 - 144.65: 1 Bond angle restraints: 11961 Sorted by residual: angle pdb=" N LEU R 256 " pdb=" CA LEU R 256 " pdb=" C LEU R 256 " ideal model delta sigma weight residual 111.14 120.33 -9.19 1.08e+00 8.57e-01 7.24e+01 angle pdb=" CA LEU B 4 " pdb=" CB LEU B 4 " pdb=" CG LEU B 4 " ideal model delta sigma weight residual 116.30 144.65 -28.35 3.50e+00 8.16e-02 6.56e+01 angle pdb=" N SER R 253 " pdb=" CA SER R 253 " pdb=" C SER R 253 " ideal model delta sigma weight residual 111.28 119.10 -7.82 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N ILE R 260 " pdb=" CA ILE R 260 " pdb=" C ILE R 260 " ideal model delta sigma weight residual 110.72 117.16 -6.44 1.01e+00 9.80e-01 4.07e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 116.86 -6.14 1.01e+00 9.80e-01 3.70e+01 ... (remaining 11956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4805 17.95 - 35.89: 364 35.89 - 53.84: 55 53.84 - 71.79: 9 71.79 - 89.73: 6 Dihedral angle restraints: 5239 sinusoidal: 2053 harmonic: 3186 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 163.36 -70.36 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 145.57 34.43 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.91 -47.91 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 5236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1181 0.096 - 0.191: 148 0.191 - 0.287: 22 0.287 - 0.382: 7 0.382 - 0.478: 5 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA HIS R 261 " pdb=" N HIS R 261 " pdb=" C HIS R 261 " pdb=" CB HIS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA ARG R 140 " pdb=" N ARG R 140 " pdb=" C ARG R 140 " pdb=" CB ARG R 140 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 1360 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " 0.038 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" CG HIS B 142 " -0.075 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.062 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO G 53 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO G 55 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.041 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 3493 2.92 - 3.58: 11901 3.58 - 4.24: 20470 4.24 - 4.90: 34846 Nonbonded interactions: 70713 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 1.600 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP R 75 " pdb=" CB SER R 272 " model vdw 2.247 3.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.284 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.287 2.440 ... (remaining 70708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.340 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.380 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 8823 Z= 0.579 Angle : 1.255 28.352 11961 Z= 0.682 Chirality : 0.073 0.478 1363 Planarity : 0.008 0.093 1498 Dihedral : 13.105 89.733 3173 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.75 % Allowed : 1.39 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.72 (0.23), residues: 1089 helix: -0.86 (0.24), residues: 374 sheet: -0.71 (0.29), residues: 283 loop : -1.52 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.035 0.003 HIS B 142 PHE 0.022 0.003 PHE B 199 TYR 0.027 0.003 TYR B 105 ARG 0.023 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7634 (t0) cc_final: 0.7096 (t0) REVERT: S 65 LYS cc_start: 0.8674 (tptp) cc_final: 0.8340 (tppp) REVERT: R 77 LEU cc_start: 0.8265 (mt) cc_final: 0.7942 (mt) REVERT: R 242 GLN cc_start: 0.8159 (pp30) cc_final: 0.7682 (pp30) outliers start: 7 outliers final: 2 residues processed: 214 average time/residue: 1.3567 time to fit residues: 306.4678 Evaluate side-chains 142 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain S residue 189 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 294 ASN A 304 GLN B 17 GLN B 35 ASN B 266 HIS G 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8823 Z= 0.295 Angle : 0.711 15.692 11961 Z= 0.344 Chirality : 0.045 0.302 1363 Planarity : 0.005 0.049 1498 Dihedral : 7.550 113.940 1257 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.99 % Allowed : 14.19 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1089 helix: 0.67 (0.26), residues: 376 sheet: -0.24 (0.30), residues: 297 loop : -1.06 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.020 0.001 HIS B 142 PHE 0.021 0.001 PHE R 39 TYR 0.028 0.002 TYR R 222 ARG 0.008 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.058 Fit side-chains REVERT: A 21 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7962 (ttp-110) REVERT: A 193 ASP cc_start: 0.7687 (t0) cc_final: 0.7339 (t0) REVERT: B 15 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8823 (ttpp) REVERT: B 156 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: B 197 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7347 (tpm-80) REVERT: B 215 GLU cc_start: 0.7482 (pt0) cc_final: 0.7275 (pt0) REVERT: G 13 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7925 (mtt90) REVERT: R 39 PHE cc_start: 0.7873 (t80) cc_final: 0.7608 (t80) outliers start: 28 outliers final: 14 residues processed: 182 average time/residue: 1.3447 time to fit residues: 259.4120 Evaluate side-chains 156 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 294 ASN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8823 Z= 0.320 Angle : 0.677 16.177 11961 Z= 0.323 Chirality : 0.044 0.304 1363 Planarity : 0.004 0.042 1498 Dihedral : 6.671 82.853 1253 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.27 % Allowed : 17.40 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1089 helix: 1.49 (0.27), residues: 376 sheet: -0.10 (0.30), residues: 295 loop : -0.84 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 154 HIS 0.021 0.002 HIS B 142 PHE 0.015 0.001 PHE R 39 TYR 0.025 0.002 TYR R 222 ARG 0.008 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.040 Fit side-chains REVERT: A 29 LYS cc_start: 0.8465 (tppp) cc_final: 0.8193 (ttmm) REVERT: A 193 ASP cc_start: 0.7677 (t0) cc_final: 0.7323 (t0) REVERT: A 310 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 10 GLU cc_start: 0.8421 (tt0) cc_final: 0.8114 (tp30) REVERT: B 197 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7331 (tpm-80) REVERT: R 39 PHE cc_start: 0.7842 (t80) cc_final: 0.7571 (t80) outliers start: 40 outliers final: 16 residues processed: 179 average time/residue: 1.3065 time to fit residues: 248.1075 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8823 Z= 0.242 Angle : 0.621 15.399 11961 Z= 0.296 Chirality : 0.043 0.293 1363 Planarity : 0.003 0.040 1498 Dihedral : 6.534 83.100 1253 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.84 % Allowed : 21.56 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1089 helix: 1.93 (0.27), residues: 374 sheet: -0.02 (0.30), residues: 292 loop : -0.69 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE R 39 TYR 0.022 0.002 TYR R 222 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 1.022 Fit side-chains REVERT: A 21 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7905 (ttp-110) REVERT: A 29 LYS cc_start: 0.8453 (tppp) cc_final: 0.8196 (ttmm) REVERT: A 193 ASP cc_start: 0.7690 (t0) cc_final: 0.7159 (t0) REVERT: A 310 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 197 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7302 (tpm-80) REVERT: G 13 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8077 (mtt90) REVERT: R 39 PHE cc_start: 0.7844 (t80) cc_final: 0.7584 (t80) REVERT: R 234 LEU cc_start: 0.8527 (mt) cc_final: 0.7651 (tm) outliers start: 36 outliers final: 15 residues processed: 174 average time/residue: 1.2255 time to fit residues: 226.8803 Evaluate side-chains 162 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8823 Z= 0.250 Angle : 0.635 15.169 11961 Z= 0.302 Chirality : 0.043 0.291 1363 Planarity : 0.003 0.045 1498 Dihedral : 6.528 83.399 1253 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.84 % Allowed : 23.05 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1089 helix: 2.10 (0.27), residues: 375 sheet: 0.00 (0.31), residues: 280 loop : -0.54 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 154 HIS 0.002 0.001 HIS A 322 PHE 0.011 0.001 PHE R 39 TYR 0.020 0.001 TYR R 222 ARG 0.009 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 0.919 Fit side-chains REVERT: A 21 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7965 (mtm-85) REVERT: A 29 LYS cc_start: 0.8456 (tppp) cc_final: 0.8144 (ttmm) REVERT: A 193 ASP cc_start: 0.7704 (t0) cc_final: 0.7355 (t0) REVERT: A 310 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8851 (mm) REVERT: B 197 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7308 (tpm-80) REVERT: R 39 PHE cc_start: 0.7866 (t80) cc_final: 0.7607 (t80) REVERT: R 234 LEU cc_start: 0.8493 (mt) cc_final: 0.7645 (tm) outliers start: 36 outliers final: 17 residues processed: 181 average time/residue: 1.2023 time to fit residues: 231.4555 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 241 ASN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8823 Z= 0.160 Angle : 0.599 12.365 11961 Z= 0.284 Chirality : 0.042 0.278 1363 Planarity : 0.003 0.050 1498 Dihedral : 6.424 82.952 1253 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.52 % Allowed : 23.69 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1089 helix: 2.33 (0.27), residues: 375 sheet: 0.15 (0.31), residues: 276 loop : -0.45 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 154 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE R 81 TYR 0.018 0.001 TYR R 222 ARG 0.010 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.035 Fit side-chains REVERT: A 21 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7951 (mtm-85) REVERT: A 29 LYS cc_start: 0.8429 (tppp) cc_final: 0.8145 (ttmm) REVERT: A 193 ASP cc_start: 0.7722 (t0) cc_final: 0.7289 (t0) REVERT: B 258 ASP cc_start: 0.8288 (t0) cc_final: 0.7683 (t0) REVERT: R 39 PHE cc_start: 0.7852 (t80) cc_final: 0.7639 (t80) REVERT: R 234 LEU cc_start: 0.8422 (mt) cc_final: 0.7556 (tm) outliers start: 33 outliers final: 11 residues processed: 182 average time/residue: 1.3262 time to fit residues: 257.8249 Evaluate side-chains 156 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8823 Z= 0.229 Angle : 0.645 13.781 11961 Z= 0.302 Chirality : 0.043 0.275 1363 Planarity : 0.004 0.052 1498 Dihedral : 6.505 83.215 1253 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.42 % Allowed : 24.55 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.06 (0.26), residues: 1089 helix: 2.40 (0.27), residues: 375 sheet: 0.20 (0.31), residues: 275 loop : -0.43 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 154 HIS 0.002 0.001 HIS B 311 PHE 0.009 0.001 PHE R 39 TYR 0.016 0.001 TYR R 222 ARG 0.012 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.043 Fit side-chains REVERT: A 21 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7931 (ttp-110) REVERT: A 29 LYS cc_start: 0.8434 (tppp) cc_final: 0.8151 (ttmm) REVERT: A 193 ASP cc_start: 0.7648 (t0) cc_final: 0.7331 (t0) REVERT: A 287 TYR cc_start: 0.7699 (m-80) cc_final: 0.7403 (m-80) REVERT: A 310 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8817 (mm) REVERT: B 258 ASP cc_start: 0.8358 (t0) cc_final: 0.7725 (t0) REVERT: R 39 PHE cc_start: 0.7860 (t80) cc_final: 0.7630 (t80) REVERT: R 201 SER cc_start: 0.8254 (m) cc_final: 0.7907 (t) REVERT: R 226 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tm) REVERT: R 234 LEU cc_start: 0.8518 (mt) cc_final: 0.7685 (tm) outliers start: 32 outliers final: 19 residues processed: 176 average time/residue: 1.1614 time to fit residues: 218.3497 Evaluate side-chains 170 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8823 Z= 0.169 Angle : 0.618 12.649 11961 Z= 0.291 Chirality : 0.042 0.252 1363 Planarity : 0.003 0.041 1498 Dihedral : 6.223 83.061 1253 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.67 % Allowed : 26.15 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.17 (0.26), residues: 1089 helix: 2.44 (0.27), residues: 378 sheet: 0.24 (0.31), residues: 277 loop : -0.30 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 154 HIS 0.002 0.000 HIS S 35 PHE 0.009 0.001 PHE R 104 TYR 0.014 0.001 TYR R 222 ARG 0.010 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.043 Fit side-chains REVERT: A 21 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7932 (ttp-110) REVERT: A 29 LYS cc_start: 0.8418 (tppp) cc_final: 0.8177 (ttmm) REVERT: A 193 ASP cc_start: 0.7661 (t0) cc_final: 0.7345 (t0) REVERT: A 287 TYR cc_start: 0.7545 (m-80) cc_final: 0.7319 (m-80) REVERT: A 310 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 226 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7930 (mp0) REVERT: B 258 ASP cc_start: 0.8240 (t0) cc_final: 0.7714 (t0) REVERT: R 39 PHE cc_start: 0.7844 (t80) cc_final: 0.7622 (t80) REVERT: R 201 SER cc_start: 0.8298 (m) cc_final: 0.7956 (t) REVERT: R 226 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (tm) outliers start: 25 outliers final: 15 residues processed: 170 average time/residue: 1.1124 time to fit residues: 202.3948 Evaluate side-chains 165 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 76 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.9486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8823 Z= 0.178 Angle : 0.639 14.039 11961 Z= 0.297 Chirality : 0.042 0.215 1363 Planarity : 0.004 0.056 1498 Dihedral : 5.638 82.850 1253 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.67 % Allowed : 26.25 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1089 helix: 2.42 (0.27), residues: 380 sheet: 0.26 (0.31), residues: 277 loop : -0.26 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 154 HIS 0.004 0.000 HIS B 142 PHE 0.009 0.001 PHE R 232 TYR 0.013 0.001 TYR R 222 ARG 0.014 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.142 Fit side-chains REVERT: A 21 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7931 (ttp-110) REVERT: A 29 LYS cc_start: 0.8421 (tppp) cc_final: 0.8150 (ttmm) REVERT: A 193 ASP cc_start: 0.7696 (t0) cc_final: 0.7351 (t0) REVERT: A 310 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8825 (mm) REVERT: B 226 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7938 (mp0) REVERT: B 258 ASP cc_start: 0.8208 (t0) cc_final: 0.7669 (t0) REVERT: R 39 PHE cc_start: 0.7812 (t80) cc_final: 0.7598 (t80) REVERT: R 201 SER cc_start: 0.8323 (m) cc_final: 0.7954 (t) REVERT: R 226 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8438 (tm) outliers start: 25 outliers final: 16 residues processed: 174 average time/residue: 1.1872 time to fit residues: 220.1218 Evaluate side-chains 166 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN A 306 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8823 Z= 0.196 Angle : 0.647 13.298 11961 Z= 0.305 Chirality : 0.042 0.229 1363 Planarity : 0.003 0.048 1498 Dihedral : 5.328 83.068 1253 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.67 % Allowed : 26.79 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1089 helix: 2.40 (0.27), residues: 380 sheet: 0.29 (0.31), residues: 277 loop : -0.24 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 154 HIS 0.003 0.000 HIS B 142 PHE 0.008 0.001 PHE R 104 TYR 0.017 0.001 TYR A 287 ARG 0.011 0.001 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.104 Fit side-chains REVERT: A 21 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7934 (ttp-110) REVERT: A 29 LYS cc_start: 0.8421 (tppp) cc_final: 0.8165 (ttmm) REVERT: A 193 ASP cc_start: 0.7701 (t0) cc_final: 0.7349 (t0) REVERT: A 310 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (mm) REVERT: B 226 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7942 (mp0) REVERT: B 258 ASP cc_start: 0.8224 (t0) cc_final: 0.7691 (t0) REVERT: G 50 LEU cc_start: 0.9066 (mt) cc_final: 0.8828 (mp) REVERT: R 39 PHE cc_start: 0.7823 (t80) cc_final: 0.7606 (t80) REVERT: R 201 SER cc_start: 0.8315 (m) cc_final: 0.7940 (t) REVERT: R 226 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (tm) outliers start: 25 outliers final: 17 residues processed: 165 average time/residue: 1.2408 time to fit residues: 217.6736 Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN A 306 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088805 restraints weight = 12824.579| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.28 r_work: 0.2935 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8823 Z= 0.167 Angle : 0.626 13.040 11961 Z= 0.294 Chirality : 0.041 0.190 1363 Planarity : 0.004 0.057 1498 Dihedral : 5.112 82.896 1253 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.35 % Allowed : 27.21 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.25 (0.26), residues: 1089 helix: 2.37 (0.27), residues: 379 sheet: 0.36 (0.31), residues: 275 loop : -0.17 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 154 HIS 0.003 0.000 HIS B 142 PHE 0.008 0.001 PHE R 104 TYR 0.012 0.001 TYR R 222 ARG 0.014 0.001 ARG S 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.58 seconds wall clock time: 73 minutes 13.59 seconds (4393.59 seconds total)