Starting phenix.real_space_refine on Thu Mar 14 14:06:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/03_2024/8w8r_37357_neut_updated.pdb" } resolution = 3.3 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5759 2.51 5 N 1552 2.21 5 O 1644 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9018 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1955 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2572 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} 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: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2223 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1782 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'U7D': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 9018 At special positions: 0 Unit cell: (125.8, 123.25, 96.05, 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 57 16.00 F 6 9.00 O 1644 8.00 N 1552 7.00 C 5759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 32.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.621A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'R' and resid 29 through 58 removed outlier: 3.817A pdb=" N VAL R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 92 removed outlier: 3.848A pdb=" N ASP R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) Proline residue: R 86 - end of helix removed outlier: 3.869A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.807A pdb=" N VAL R 108 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 139 No H-bonds generated for 'chain 'R' and resid 137 through 139' Processing helix chain 'R' and resid 145 through 167 Proline residue: R 165 - end of helix Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'R' and resid 202 through 227 removed outlier: 4.156A pdb=" N VAL R 214 " --> pdb=" O ALA R 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 424 Proline residue: R 414 - end of helix removed outlier: 4.034A pdb=" N VAL R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 444 removed outlier: 3.731A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 454 Proline residue: R 451 - end of helix Processing helix chain 'R' and resid 459 through 472 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 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 11 through 23 removed outlier: 3.796A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.984A pdb=" N ALA A 253 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL A 234 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY A 57 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.035A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.877A 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: 7.147A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 152 removed outlier: 6.799A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.989A 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: 6.646A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.115A 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: 6.875A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 172 through 174 removed outlier: 4.407A pdb=" N GLN R 172 " --> pdb=" O ILE R 185 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'S' and resid 92 through 99 removed outlier: 3.648A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.911A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1104 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: 2.42 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1461 1.32 - 1.45: 2593 1.45 - 1.57: 5084 1.57 - 1.70: 2 1.70 - 1.83: 79 Bond restraints: 9219 Sorted by residual: bond pdb=" N LEU B 308 " pdb=" CA LEU B 308 " ideal model delta sigma weight residual 1.455 1.516 -0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" CA SER B 191 " pdb=" CB SER B 191 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.69e-02 3.50e+03 1.70e+01 bond pdb=" N VAL R 425 " pdb=" CA VAL R 425 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.23e-02 6.61e+03 1.30e+01 bond pdb=" N ALA B 309 " pdb=" CA ALA B 309 " ideal model delta sigma weight residual 1.461 1.507 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" C PRO B 107 " pdb=" O PRO B 107 " ideal model delta sigma weight residual 1.237 1.194 0.044 1.26e-02 6.30e+03 1.20e+01 ... (remaining 9214 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.32: 288 107.32 - 114.15: 5224 114.15 - 120.99: 4183 120.99 - 127.82: 2733 127.82 - 134.66: 85 Bond angle restraints: 12513 Sorted by residual: angle pdb=" N PRO R 165 " pdb=" CA PRO R 165 " pdb=" C PRO R 165 " ideal model delta sigma weight residual 110.70 119.95 -9.25 1.22e+00 6.72e-01 5.75e+01 angle pdb=" CA ILE B 232 " pdb=" C ILE B 232 " pdb=" O ILE B 232 " ideal model delta sigma weight residual 120.96 116.19 4.77 8.40e-01 1.42e+00 3.22e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 107.73 114.61 -6.88 1.34e+00 5.57e-01 2.63e+01 angle pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" O GLY B 310 " ideal model delta sigma weight residual 119.01 124.56 -5.55 1.11e+00 8.12e-01 2.50e+01 angle pdb=" N THR R 105 " pdb=" CA THR R 105 " pdb=" C THR R 105 " ideal model delta sigma weight residual 113.50 107.50 6.00 1.23e+00 6.61e-01 2.38e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4671 17.55 - 35.11: 582 35.11 - 52.66: 148 52.66 - 70.22: 32 70.22 - 87.77: 9 Dihedral angle restraints: 5442 sinusoidal: 2115 harmonic: 3327 Sorted by residual: dihedral pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta harmonic sigma weight residual 122.80 113.13 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual -86.00 -117.74 31.74 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1180 0.067 - 0.134: 189 0.134 - 0.200: 32 0.200 - 0.267: 12 0.267 - 0.334: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1412 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 307 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL B 307 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL B 307 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 308 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO S 236 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C PRO S 236 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO S 236 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU S 237 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 234 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C PHE B 234 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE B 234 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1383 2.76 - 3.30: 7828 3.30 - 3.83: 13707 3.83 - 4.37: 15971 4.37 - 4.90: 29542 Nonbonded interactions: 68431 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.227 2.440 nonbonded pdb=" O THR S 144 " pdb=" OG1 THR S 243 " model vdw 2.250 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.289 2.440 nonbonded pdb=" O LEU A 346 " pdb=" OG1 THR A 350 " model vdw 2.294 2.440 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.306 2.520 ... (remaining 68426 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.840 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.740 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 0.070 9219 Z= 0.375 Angle : 0.817 9.253 12513 Z= 0.553 Chirality : 0.056 0.334 1415 Planarity : 0.005 0.049 1577 Dihedral : 16.728 87.770 3285 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.64 % Allowed : 22.87 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1126 helix: 1.42 (0.28), residues: 368 sheet: 0.60 (0.33), residues: 251 loop : -1.78 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.001 PHE B 241 TYR 0.012 0.002 TYR A 47 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.094 Fit side-chains REVERT: B 251 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7456 (mtt90) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.2820 time to fit residues: 37.3190 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 425 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9219 Z= 0.193 Angle : 0.549 8.849 12513 Z= 0.292 Chirality : 0.043 0.139 1415 Planarity : 0.004 0.042 1577 Dihedral : 5.616 59.683 1264 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.08 % Allowed : 23.08 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1126 helix: 1.69 (0.27), residues: 371 sheet: 0.26 (0.31), residues: 280 loop : -1.67 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE B 241 TYR 0.018 0.001 TYR S 235 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.084 Fit side-chains REVERT: A 297 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7110 (tp) REVERT: B 119 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8839 (m-40) REVERT: R 470 LYS cc_start: 0.5856 (mptt) cc_final: 0.5110 (tttp) outliers start: 30 outliers final: 21 residues processed: 113 average time/residue: 0.2551 time to fit residues: 38.4040 Evaluate side-chains 108 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 40.0000 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9219 Z= 0.263 Angle : 0.594 9.137 12513 Z= 0.316 Chirality : 0.044 0.159 1415 Planarity : 0.004 0.043 1577 Dihedral : 5.319 57.444 1256 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.13 % Allowed : 22.15 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1126 helix: 1.56 (0.27), residues: 372 sheet: 0.17 (0.31), residues: 281 loop : -1.71 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE B 234 TYR 0.019 0.002 TYR S 235 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 93 time to evaluate : 1.003 Fit side-chains REVERT: A 223 GLN cc_start: 0.8640 (tt0) cc_final: 0.8426 (tt0) REVERT: A 297 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7132 (tp) REVERT: B 151 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7696 (t80) REVERT: B 186 ASP cc_start: 0.8093 (p0) cc_final: 0.7768 (p0) REVERT: B 259 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: R 102 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4924 (t70) REVERT: R 470 LYS cc_start: 0.5832 (mptt) cc_final: 0.5114 (tttp) outliers start: 50 outliers final: 34 residues processed: 135 average time/residue: 0.2591 time to fit residues: 45.9610 Evaluate side-chains 129 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain Y residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9219 Z= 0.372 Angle : 0.668 10.032 12513 Z= 0.353 Chirality : 0.047 0.201 1415 Planarity : 0.005 0.049 1577 Dihedral : 5.583 54.857 1255 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.44 % Allowed : 22.46 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1126 helix: 1.27 (0.27), residues: 370 sheet: 0.12 (0.30), residues: 283 loop : -1.78 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.008 0.002 HIS A 357 PHE 0.018 0.002 PHE B 241 TYR 0.020 0.002 TYR A 47 ARG 0.004 0.000 ARG R 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 91 time to evaluate : 0.831 Fit side-chains REVERT: A 297 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7165 (tp) REVERT: B 151 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7642 (t80) REVERT: B 186 ASP cc_start: 0.8228 (p0) cc_final: 0.7907 (p0) REVERT: B 259 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: R 102 HIS cc_start: 0.5594 (OUTLIER) cc_final: 0.4890 (t70) REVERT: R 470 LYS cc_start: 0.6015 (mptt) cc_final: 0.5278 (tttp) outliers start: 53 outliers final: 41 residues processed: 134 average time/residue: 0.2387 time to fit residues: 42.6753 Evaluate side-chains 134 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 89 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9219 Z= 0.226 Angle : 0.563 9.984 12513 Z= 0.299 Chirality : 0.043 0.149 1415 Planarity : 0.004 0.043 1577 Dihedral : 5.194 58.781 1252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.92 % Allowed : 22.97 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1126 helix: 1.49 (0.27), residues: 371 sheet: 0.28 (0.31), residues: 272 loop : -1.81 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.015 0.002 TYR S 235 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 91 time to evaluate : 1.057 Fit side-chains REVERT: A 45 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8188 (tp-100) REVERT: A 297 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7200 (tp) REVERT: B 151 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 186 ASP cc_start: 0.8208 (p0) cc_final: 0.7852 (p0) REVERT: B 217 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7562 (ptt) REVERT: B 259 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: R 470 LYS cc_start: 0.6065 (mptt) cc_final: 0.5244 (tttp) outliers start: 48 outliers final: 38 residues processed: 131 average time/residue: 0.2371 time to fit residues: 41.8970 Evaluate side-chains 131 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 89 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain Y residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 0.0050 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 40.0000 chunk 104 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9219 Z= 0.228 Angle : 0.565 9.649 12513 Z= 0.300 Chirality : 0.043 0.153 1415 Planarity : 0.004 0.050 1577 Dihedral : 5.130 57.439 1252 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.54 % Allowed : 22.46 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1126 helix: 1.56 (0.27), residues: 371 sheet: 0.18 (0.31), residues: 279 loop : -1.77 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.016 0.002 TYR A 47 ARG 0.004 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 91 time to evaluate : 1.052 Fit side-chains REVERT: A 297 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7191 (tp) REVERT: B 151 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 186 ASP cc_start: 0.8203 (p0) cc_final: 0.7794 (p0) REVERT: B 217 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7576 (ptt) REVERT: B 259 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: R 102 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.5056 (t70) REVERT: R 470 LYS cc_start: 0.6170 (mptt) cc_final: 0.5250 (tttp) outliers start: 54 outliers final: 44 residues processed: 138 average time/residue: 0.2472 time to fit residues: 45.2624 Evaluate side-chains 141 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 92 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9219 Z= 0.131 Angle : 0.489 8.819 12513 Z= 0.260 Chirality : 0.041 0.147 1415 Planarity : 0.003 0.042 1577 Dihedral : 4.753 54.548 1252 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.49 % Allowed : 24.92 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1126 helix: 1.89 (0.27), residues: 371 sheet: 0.24 (0.31), residues: 282 loop : -1.78 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR A 47 ARG 0.004 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.201 Fit side-chains REVERT: B 151 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 186 ASP cc_start: 0.8075 (p0) cc_final: 0.7548 (p0) REVERT: B 259 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: R 102 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.4995 (t70) REVERT: R 470 LYS cc_start: 0.6081 (mptt) cc_final: 0.5229 (tttp) outliers start: 34 outliers final: 25 residues processed: 127 average time/residue: 0.2566 time to fit residues: 43.2597 Evaluate side-chains 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9219 Z= 0.213 Angle : 0.550 9.015 12513 Z= 0.291 Chirality : 0.043 0.151 1415 Planarity : 0.004 0.049 1577 Dihedral : 4.872 52.108 1252 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.59 % Allowed : 24.92 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1126 helix: 1.82 (0.27), residues: 373 sheet: 0.20 (0.31), residues: 280 loop : -1.69 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE B 241 TYR 0.016 0.002 TYR A 47 ARG 0.004 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 0.982 Fit side-chains REVERT: B 43 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7373 (mm) REVERT: B 151 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 186 ASP cc_start: 0.8203 (p0) cc_final: 0.7688 (p0) REVERT: B 217 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7509 (ptt) REVERT: B 259 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: R 102 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.5053 (t70) REVERT: R 470 LYS cc_start: 0.6084 (mptt) cc_final: 0.5260 (tttp) REVERT: S 109 ASP cc_start: 0.9028 (p0) cc_final: 0.8673 (p0) outliers start: 35 outliers final: 29 residues processed: 122 average time/residue: 0.2542 time to fit residues: 41.3808 Evaluate side-chains 126 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.2980 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9219 Z= 0.193 Angle : 0.532 8.948 12513 Z= 0.282 Chirality : 0.042 0.155 1415 Planarity : 0.004 0.045 1577 Dihedral : 4.829 51.462 1252 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.00 % Allowed : 24.41 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1126 helix: 1.88 (0.27), residues: 372 sheet: 0.16 (0.31), residues: 285 loop : -1.67 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE B 241 TYR 0.014 0.001 TYR A 47 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 0.820 Fit side-chains REVERT: B 43 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7369 (mm) REVERT: B 151 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 186 ASP cc_start: 0.8210 (p0) cc_final: 0.7681 (p0) REVERT: B 217 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (ptt) REVERT: B 259 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: R 91 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6901 (p) REVERT: R 102 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.5101 (t70) REVERT: R 470 LYS cc_start: 0.5959 (mptt) cc_final: 0.5144 (tttp) REVERT: S 109 ASP cc_start: 0.9020 (p0) cc_final: 0.8609 (p0) outliers start: 39 outliers final: 31 residues processed: 126 average time/residue: 0.2774 time to fit residues: 46.8707 Evaluate side-chains 128 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9219 Z= 0.119 Angle : 0.468 8.069 12513 Z= 0.248 Chirality : 0.040 0.152 1415 Planarity : 0.003 0.042 1577 Dihedral : 4.432 50.290 1252 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 26.15 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1126 helix: 2.22 (0.27), residues: 372 sheet: 0.31 (0.31), residues: 282 loop : -1.73 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.007 0.001 TYR S 190 ARG 0.005 0.000 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.818 Fit side-chains REVERT: B 151 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 259 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: R 102 HIS cc_start: 0.5793 (OUTLIER) cc_final: 0.5202 (t70) REVERT: R 470 LYS cc_start: 0.5991 (mptt) cc_final: 0.5172 (tttp) REVERT: S 109 ASP cc_start: 0.8913 (p0) cc_final: 0.8470 (p0) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.2472 time to fit residues: 41.3738 Evaluate side-chains 122 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123938 restraints weight = 10201.096| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.78 r_work: 0.3059 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9219 Z= 0.169 Angle : 0.527 13.098 12513 Z= 0.273 Chirality : 0.042 0.181 1415 Planarity : 0.004 0.045 1577 Dihedral : 4.528 49.728 1252 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.67 % Allowed : 25.74 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1126 helix: 2.15 (0.27), residues: 373 sheet: 0.22 (0.31), residues: 288 loop : -1.65 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE A 222 TYR 0.014 0.001 TYR A 47 ARG 0.005 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.19 seconds wall clock time: 37 minutes 17.34 seconds (2237.34 seconds total)