Starting phenix.real_space_refine on Wed Feb 14 09:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfx_31962/02_2024/7vfx_31962_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 64 5.16 5 C 5781 2.51 5 N 1512 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 54": "NH1" <-> "NH2" Residue "R PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 269": "NH1" <-> "NH2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 3, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.45, per 1000 atoms: 0.61 Number of scatterers: 9004 At special positions: 0 Unit cell: (90.1, 124.95, 123.25, 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 64 16.00 O 1647 8.00 N 1512 7.00 C 5781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 3.54 Conformation dependent library (CDL) restraints added in 2.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 59 through 86 removed outlier: 4.585A pdb=" N THR R 77 " --> pdb=" O CYS R 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 95 through 128 Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 163 removed outlier: 4.111A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 187 through 208 removed outlier: 4.145A pdb=" N ASN R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 237 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 removed outlier: 4.193A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 302 removed outlier: 4.218A pdb=" N ALA R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 314 Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.977A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 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 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.078A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 4.106A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.496A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 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 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'R' and resid 164 through 169 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.678A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.906A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.894A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.738A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.956A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.751A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.610A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.710A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (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 13 removed outlier: 3.658A pdb=" N SER S 120 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 243 through 245 removed outlier: 3.630A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG S 180 " --> pdb=" O PRO S 185 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1197 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: 2.85 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2864 1.34 - 1.46: 2238 1.46 - 1.58: 4003 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9200 Sorted by residual: bond pdb=" SD FME C 1 " pdb=" CE FME C 1 " ideal model delta sigma weight residual 1.805 1.750 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" CG FME C 1 " pdb=" SD FME C 1 " ideal model delta sigma weight residual 1.817 1.771 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" N FME C 1 " pdb=" CN FME C 1 " ideal model delta sigma weight residual 1.335 1.374 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.72e-02 3.38e+03 3.45e+00 bond pdb=" C10 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.551 1.517 0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 9195 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.38: 206 106.38 - 113.29: 5065 113.29 - 120.19: 3297 120.19 - 127.09: 3806 127.09 - 133.99: 97 Bond angle restraints: 12471 Sorted by residual: angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.73 3.47 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CB MET R 197 " pdb=" CG MET R 197 " pdb=" SD MET R 197 " ideal model delta sigma weight residual 112.70 121.18 -8.48 3.00e+00 1.11e-01 7.98e+00 angle pdb=" CA VAL R 302 " pdb=" C VAL R 302 " pdb=" N PHE R 303 " ideal model delta sigma weight residual 116.60 120.42 -3.82 1.45e+00 4.76e-01 6.94e+00 angle pdb=" CA CYS S 96 " pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 114.40 120.19 -5.79 2.30e+00 1.89e-01 6.33e+00 angle pdb=" C MET A 240 " pdb=" N ASN A 241 " pdb=" CA ASN A 241 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.32e+00 ... (remaining 12466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 5263 24.42 - 48.83: 275 48.83 - 73.25: 34 73.25 - 97.67: 12 97.67 - 122.08: 1 Dihedral angle restraints: 5585 sinusoidal: 2300 harmonic: 3285 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLN S 142 " pdb=" C GLN S 142 " pdb=" N ALA S 143 " pdb=" CA ALA S 143 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C10 CLR R 403 " pdb=" C1 CLR R 403 " pdb=" C2 CLR R 403 " pdb=" C3 CLR R 403 " ideal model delta sinusoidal sigma weight residual -56.83 65.25 -122.08 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 992 0.042 - 0.084: 324 0.084 - 0.127: 94 0.127 - 0.169: 12 0.169 - 0.211: 7 Chirality restraints: 1429 Sorted by residual: chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.74 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.75 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1426 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO S 148 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 158 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO R 159 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " 0.024 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1356 2.76 - 3.29: 8287 3.29 - 3.83: 14407 3.83 - 4.36: 17311 4.36 - 4.90: 30489 Nonbonded interactions: 71850 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP B 153 " pdb=" NE2 GLN B 156 " model vdw 2.292 2.520 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.300 2.520 nonbonded pdb=" O GLY S 112 " pdb=" OG SER S 184 " model vdw 2.333 2.440 nonbonded pdb=" NZ LYS S 163 " pdb=" OE2 GLU S 234 " model vdw 2.336 2.520 ... (remaining 71845 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: 1.290 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: 4.140 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.003 0.055 9200 Z= 0.227 Angle : 0.654 8.477 12471 Z= 0.351 Chirality : 0.046 0.211 1429 Planarity : 0.004 0.094 1552 Dihedral : 15.033 122.082 3456 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.41 (0.25), residues: 1120 helix: 1.62 (0.27), residues: 400 sheet: 0.28 (0.30), residues: 287 loop : -0.99 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE B 199 TYR 0.011 0.001 TYR S 190 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.084 Fit side-chains REVERT: R 44 ASN cc_start: 0.8230 (m110) cc_final: 0.7988 (m110) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.4588 time to fit residues: 185.3637 Evaluate side-chains 100 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 108 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9200 Z= 0.193 Angle : 0.554 7.460 12471 Z= 0.289 Chirality : 0.043 0.143 1429 Planarity : 0.004 0.040 1552 Dihedral : 7.325 59.609 1436 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.34 % Allowed : 7.22 % Favored : 91.44 % 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: 0.65 (0.25), residues: 1120 helix: 1.88 (0.27), residues: 398 sheet: 0.43 (0.31), residues: 275 loop : -0.88 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR S 190 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.037 Fit side-chains REVERT: A 242 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7130 (mtp180) REVERT: G 19 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5666 (mp) outliers start: 13 outliers final: 0 residues processed: 107 average time/residue: 1.4259 time to fit residues: 161.6569 Evaluate side-chains 102 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 108 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9200 Z= 0.182 Angle : 0.528 7.741 12471 Z= 0.279 Chirality : 0.042 0.141 1429 Planarity : 0.003 0.037 1552 Dihedral : 6.654 58.358 1436 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.34 % Allowed : 9.38 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1120 helix: 2.03 (0.27), residues: 397 sheet: 0.44 (0.31), residues: 277 loop : -0.86 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.014 0.001 TYR A 287 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.082 Fit side-chains REVERT: R 183 TRP cc_start: 0.6591 (p90) cc_final: 0.6296 (p90) REVERT: A 242 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: B 217 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6436 (pp-130) REVERT: G 19 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5573 (mp) REVERT: S 234 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: S 245 LEU cc_start: 0.8699 (tt) cc_final: 0.8498 (tp) outliers start: 13 outliers final: 3 residues processed: 110 average time/residue: 1.3795 time to fit residues: 161.2191 Evaluate side-chains 106 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 108 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9200 Z= 0.224 Angle : 0.552 7.901 12471 Z= 0.291 Chirality : 0.043 0.144 1429 Planarity : 0.003 0.037 1552 Dihedral : 6.595 57.380 1436 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.75 % Allowed : 11.13 % Favored : 87.11 % 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: 0.78 (0.25), residues: 1120 helix: 2.00 (0.27), residues: 397 sheet: 0.45 (0.30), residues: 282 loop : -0.80 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE B 199 TYR 0.010 0.001 TYR S 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.029 Fit side-chains REVERT: R 183 TRP cc_start: 0.6586 (p90) cc_final: 0.6299 (p90) REVERT: A 242 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7104 (mtp180) REVERT: B 217 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6473 (pp-130) REVERT: G 19 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5515 (mp) REVERT: S 234 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7160 (mt-10) outliers start: 17 outliers final: 6 residues processed: 114 average time/residue: 1.4135 time to fit residues: 171.2121 Evaluate side-chains 110 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 108 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9200 Z= 0.236 Angle : 0.556 8.743 12471 Z= 0.294 Chirality : 0.043 0.144 1429 Planarity : 0.003 0.037 1552 Dihedral : 6.544 57.371 1436 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.75 % Allowed : 12.99 % Favored : 85.26 % 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: 0.74 (0.25), residues: 1120 helix: 1.91 (0.26), residues: 403 sheet: 0.49 (0.31), residues: 280 loop : -0.85 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE B 199 TYR 0.014 0.002 TYR A 287 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.092 Fit side-chains REVERT: R 90 HIS cc_start: 0.7774 (t-90) cc_final: 0.7500 (t-90) REVERT: R 183 TRP cc_start: 0.6559 (p90) cc_final: 0.6256 (p90) REVERT: A 242 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: A 311 ASN cc_start: 0.8466 (t0) cc_final: 0.8076 (t0) REVERT: B 217 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6498 (pp-130) REVERT: G 19 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5558 (mp) REVERT: S 234 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: S 245 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8345 (mp) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 1.3940 time to fit residues: 165.9242 Evaluate side-chains 113 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9200 Z= 0.129 Angle : 0.489 7.604 12471 Z= 0.258 Chirality : 0.041 0.135 1429 Planarity : 0.003 0.035 1552 Dihedral : 6.087 57.711 1436 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.75 % Allowed : 13.51 % Favored : 84.74 % 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: 0.91 (0.25), residues: 1120 helix: 2.13 (0.27), residues: 404 sheet: 0.52 (0.30), residues: 276 loop : -0.79 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.000 HIS A 188 PHE 0.013 0.001 PHE B 199 TYR 0.010 0.001 TYR S 235 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.980 Fit side-chains REVERT: R 44 ASN cc_start: 0.8272 (m110) cc_final: 0.8005 (m110) REVERT: A 311 ASN cc_start: 0.8416 (t0) cc_final: 0.8122 (t0) REVERT: G 19 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5625 (mp) REVERT: S 245 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8455 (mp) outliers start: 17 outliers final: 5 residues processed: 115 average time/residue: 1.2672 time to fit residues: 155.3866 Evaluate side-chains 108 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9200 Z= 0.136 Angle : 0.495 10.351 12471 Z= 0.259 Chirality : 0.041 0.137 1429 Planarity : 0.003 0.033 1552 Dihedral : 5.994 58.613 1436 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.44 % Allowed : 13.81 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1120 helix: 2.20 (0.26), residues: 403 sheet: 0.55 (0.30), residues: 276 loop : -0.70 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR A 287 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.007 Fit side-chains REVERT: R 44 ASN cc_start: 0.8266 (m110) cc_final: 0.7999 (m110) REVERT: A 311 ASN cc_start: 0.8453 (t0) cc_final: 0.8118 (t0) REVERT: G 19 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5591 (mp) REVERT: S 245 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (mp) outliers start: 14 outliers final: 7 residues processed: 111 average time/residue: 1.2967 time to fit residues: 153.6269 Evaluate side-chains 108 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9200 Z= 0.267 Angle : 0.578 9.854 12471 Z= 0.303 Chirality : 0.043 0.145 1429 Planarity : 0.003 0.033 1552 Dihedral : 6.443 55.501 1436 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.96 % Allowed : 14.64 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1120 helix: 2.02 (0.26), residues: 404 sheet: 0.46 (0.30), residues: 282 loop : -0.73 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.002 PHE A 189 TYR 0.011 0.002 TYR S 190 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.026 Fit side-chains REVERT: R 183 TRP cc_start: 0.6493 (p90) cc_final: 0.6121 (p90) REVERT: A 242 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7146 (mtp180) REVERT: B 217 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6016 (pp-130) REVERT: G 19 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5488 (mp) REVERT: S 245 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8500 (mp) outliers start: 19 outliers final: 5 residues processed: 115 average time/residue: 1.3458 time to fit residues: 165.3834 Evaluate side-chains 110 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9200 Z= 0.135 Angle : 0.502 10.024 12471 Z= 0.263 Chirality : 0.041 0.134 1429 Planarity : 0.003 0.033 1552 Dihedral : 6.001 58.465 1436 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 15.46 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1120 helix: 2.17 (0.26), residues: 403 sheet: 0.62 (0.30), residues: 277 loop : -0.67 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR A 287 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.060 Fit side-chains REVERT: R 183 TRP cc_start: 0.6473 (p90) cc_final: 0.6107 (p90) REVERT: A 242 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: A 311 ASN cc_start: 0.8435 (t0) cc_final: 0.8066 (t0) REVERT: B 217 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5985 (pp-130) REVERT: G 19 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5635 (mp) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 1.3434 time to fit residues: 158.8275 Evaluate side-chains 112 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 80 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9200 Z= 0.135 Angle : 0.503 10.593 12471 Z= 0.262 Chirality : 0.040 0.136 1429 Planarity : 0.003 0.035 1552 Dihedral : 5.883 58.903 1436 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.03 % Allowed : 15.98 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1120 helix: 2.24 (0.26), residues: 404 sheet: 0.58 (0.30), residues: 280 loop : -0.64 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.010 0.001 TYR S 190 ARG 0.003 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.034 Fit side-chains REVERT: A 242 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7102 (mtp180) REVERT: A 297 GLU cc_start: 0.7582 (mp0) cc_final: 0.7278 (mp0) REVERT: A 311 ASN cc_start: 0.8459 (t0) cc_final: 0.8142 (t0) REVERT: A 329 THR cc_start: 0.7711 (m) cc_final: 0.7465 (t) REVERT: B 217 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.5991 (pp-130) REVERT: G 19 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5612 (mp) REVERT: S 80 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7644 (p90) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 1.3251 time to fit residues: 152.3098 Evaluate side-chains 106 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 80 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091228 restraints weight = 12659.600| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.42 r_work: 0.2915 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9200 Z= 0.169 Angle : 0.527 10.153 12471 Z= 0.275 Chirality : 0.041 0.140 1429 Planarity : 0.003 0.034 1552 Dihedral : 6.012 58.015 1436 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.13 % Allowed : 16.29 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1120 helix: 2.21 (0.26), residues: 403 sheet: 0.53 (0.30), residues: 285 loop : -0.61 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE A 189 TYR 0.016 0.001 TYR A 287 ARG 0.006 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.54 seconds wall clock time: 62 minutes 56.32 seconds (3776.32 seconds total)