Starting phenix.real_space_refine on Fri Nov 15 07:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/11_2024/8jpn_36484.cif" } resolution = 2.9 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= 0.049 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 52 5.16 5 C 5469 2.51 5 N 1447 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2528 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 336} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 397 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2187 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "S" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1723 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'U9S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.83, per 1000 atoms: 0.80 Number of scatterers: 8557 At special positions: 0 Unit cell: (90.316, 124.69, 130.756, 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 52 16.00 O 1589 8.00 N 1447 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 172 " 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.632A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.338A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.508A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.790A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.597A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 11 through 51 removed outlier: 4.827A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.897A pdb=" N TYR R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS R 103 " --> pdb=" O ARG R 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 220 Processing helix chain 'R' and resid 227 through 259 removed outlier: 3.725A pdb=" N LEU R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.607A pdb=" N ARG R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 285 removed outlier: 3.669A pdb=" N ASN R 274 " --> pdb=" O GLN R 270 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR R 280 " --> pdb=" O PHE R 276 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) Proline residue: R 282 - end of helix removed outlier: 3.841A pdb=" N PHE R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 296 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 312 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.525A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.639A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.934A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.006A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.691A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.979A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.694A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.562A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1299 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: 2.46 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2763 1.34 - 1.46: 2216 1.46 - 1.58: 3690 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8743 Sorted by residual: bond pdb=" N VAL R 289 " pdb=" CA VAL R 289 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.04e+00 bond pdb=" N SER R 288 " pdb=" CA SER R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.33e-02 5.65e+03 5.63e+00 bond pdb=" C04 U9S R 501 " pdb=" C05 U9S R 501 " ideal model delta sigma weight residual 1.466 1.504 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" N LEU S 219 " pdb=" CA LEU S 219 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.27e-02 6.20e+03 3.52e+00 bond pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 ... (remaining 8738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11716 1.94 - 3.88: 168 3.88 - 5.82: 25 5.82 - 7.76: 5 7.76 - 9.70: 1 Bond angle restraints: 11915 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " ideal model delta sigma weight residual 114.58 117.46 -2.88 8.60e-01 1.35e+00 1.12e+01 angle pdb=" N SER R 288 " pdb=" CA SER R 288 " pdb=" C SER R 288 " ideal model delta sigma weight residual 113.28 109.26 4.02 1.22e+00 6.72e-01 1.09e+01 angle pdb=" CB MET R 251 " pdb=" CG MET R 251 " pdb=" SD MET R 251 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C SER S 217 " pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 121.54 115.82 5.72 1.91e+00 2.74e-01 8.97e+00 angle pdb=" CA CYS S 96 " pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 114.40 120.79 -6.39 2.30e+00 1.89e-01 7.73e+00 ... (remaining 11910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4490 17.06 - 34.13: 454 34.13 - 51.19: 133 51.19 - 68.25: 21 68.25 - 85.32: 9 Dihedral angle restraints: 5107 sinusoidal: 1746 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 268 " pdb=" CB CYS R 268 " ideal model delta sinusoidal sigma weight residual -86.00 -47.23 -38.77 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 808 0.030 - 0.059: 360 0.059 - 0.089: 131 0.089 - 0.118: 73 0.118 - 0.148: 16 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA VAL R 289 " pdb=" N VAL R 289 " pdb=" C VAL R 289 " pdb=" CB VAL R 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO S 236 " pdb=" N PRO S 236 " pdb=" C PRO S 236 " pdb=" CB PRO S 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1385 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO S 75 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 119 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" CG ASP R 119 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP R 119 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP R 119 " -0.010 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2107 2.79 - 3.32: 7395 3.32 - 3.85: 13568 3.85 - 4.37: 16028 4.37 - 4.90: 28748 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" O ALA R 104 " pdb=" OG1 THR R 108 " model vdw 2.268 3.040 nonbonded pdb=" O VAL R 272 " pdb=" OG SER R 275 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 3.040 nonbonded pdb=" OE1 GLU S 6 " pdb=" N GLY S 114 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.333 3.120 ... (remaining 67841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.780 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.004 0.039 8743 Z= 0.243 Angle : 0.608 9.704 11915 Z= 0.335 Chirality : 0.043 0.148 1388 Planarity : 0.004 0.067 1514 Dihedral : 15.560 85.318 2929 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.36 % Allowed : 20.90 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.11 (0.25), residues: 1141 helix: 2.43 (0.27), residues: 389 sheet: 1.04 (0.30), residues: 277 loop : -0.94 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.002 PHE R 34 TYR 0.014 0.001 TYR R 25 ARG 0.009 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.978 Fit side-chains REVERT: A 293 SER cc_start: 0.7508 (m) cc_final: 0.7123 (m) REVERT: B 212 ASP cc_start: 0.5923 (t0) cc_final: 0.5644 (t70) REVERT: R 151 THR cc_start: 0.7725 (m) cc_final: 0.7501 (p) REVERT: R 204 CYS cc_start: 0.7966 (m) cc_final: 0.7513 (m) REVERT: R 208 TYR cc_start: 0.7321 (t80) cc_final: 0.7010 (t80) outliers start: 3 outliers final: 3 residues processed: 194 average time/residue: 1.0965 time to fit residues: 228.5482 Evaluate side-chains 117 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 259 GLN R 287 ASN S 113 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8743 Z= 0.244 Angle : 0.613 6.738 11915 Z= 0.332 Chirality : 0.044 0.183 1388 Planarity : 0.005 0.049 1514 Dihedral : 4.449 28.395 1246 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.99 % Allowed : 20.07 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1141 helix: 2.62 (0.26), residues: 391 sheet: 1.26 (0.31), residues: 265 loop : -1.07 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 244 PHE 0.022 0.002 PHE R 34 TYR 0.025 0.002 TYR R 277 ARG 0.010 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.774 Fit side-chains REVERT: A 318 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: B 217 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7391 (pmt) REVERT: B 258 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: R 111 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7818 (mm) REVERT: R 131 HIS cc_start: 0.8153 (t-90) cc_final: 0.7912 (t-90) REVERT: R 151 THR cc_start: 0.7984 (m) cc_final: 0.7735 (p) REVERT: R 204 CYS cc_start: 0.8097 (m) cc_final: 0.7453 (m) REVERT: R 208 TYR cc_start: 0.7474 (t80) cc_final: 0.7106 (t80) REVERT: R 285 PHE cc_start: 0.6474 (m-10) cc_final: 0.6259 (m-80) REVERT: S 140 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: S 183 GLN cc_start: 0.8700 (mt0) cc_final: 0.8379 (mt0) outliers start: 42 outliers final: 8 residues processed: 156 average time/residue: 1.0751 time to fit residues: 180.3750 Evaluate side-chains 116 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 155 ASN B 230 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8743 Z= 0.169 Angle : 0.521 5.635 11915 Z= 0.280 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.044 1514 Dihedral : 3.933 18.748 1240 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.09 % Allowed : 23.28 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.36 (0.25), residues: 1141 helix: 2.85 (0.26), residues: 399 sheet: 0.89 (0.30), residues: 281 loop : -0.90 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 131 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR A 230 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.936 Fit side-chains REVERT: A 186 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 251 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 254 ASP cc_start: 0.8116 (p0) cc_final: 0.7877 (t0) REVERT: R 111 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7823 (mm) REVERT: R 151 THR cc_start: 0.8014 (m) cc_final: 0.7767 (p) REVERT: R 204 CYS cc_start: 0.8204 (m) cc_final: 0.7532 (m) REVERT: R 208 TYR cc_start: 0.7556 (t80) cc_final: 0.7185 (t80) REVERT: R 285 PHE cc_start: 0.6862 (m-10) cc_final: 0.6632 (m-80) REVERT: S 3 GLN cc_start: 0.7823 (mt0) cc_final: 0.7503 (mm-40) REVERT: S 18 ARG cc_start: 0.8436 (tpt-90) cc_final: 0.8215 (tpt-90) REVERT: S 183 GLN cc_start: 0.8776 (mt0) cc_final: 0.8449 (mt0) outliers start: 26 outliers final: 7 residues processed: 120 average time/residue: 1.1171 time to fit residues: 144.4752 Evaluate side-chains 109 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN R 134 GLN R 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8743 Z= 0.389 Angle : 0.715 9.068 11915 Z= 0.380 Chirality : 0.048 0.181 1388 Planarity : 0.005 0.052 1514 Dihedral : 4.799 23.380 1240 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.11 % Allowed : 20.78 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.85 (0.25), residues: 1141 helix: 2.44 (0.26), residues: 390 sheet: 0.66 (0.30), residues: 286 loop : -1.19 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS R 249 PHE 0.024 0.002 PHE R 115 TYR 0.016 0.002 TYR R 25 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.880 Fit side-chains REVERT: A 186 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: B 22 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5058 (mpt-90) REVERT: B 227 SER cc_start: 0.9454 (m) cc_final: 0.9093 (t) REVERT: B 234 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8665 (t80) REVERT: C 52 THR cc_start: 0.8049 (m) cc_final: 0.7691 (p) REVERT: R 214 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7325 (mp) outliers start: 43 outliers final: 17 residues processed: 144 average time/residue: 1.1310 time to fit residues: 174.5704 Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN R 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8743 Z= 0.160 Angle : 0.525 5.873 11915 Z= 0.283 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.052 1514 Dihedral : 4.211 18.475 1240 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.26 % Allowed : 24.11 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.18 (0.25), residues: 1141 helix: 2.74 (0.26), residues: 403 sheet: 0.78 (0.30), residues: 277 loop : -1.06 (0.27), residues: 461 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 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR S 190 ARG 0.003 0.000 ARG R 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.881 Fit side-chains REVERT: A 33 GLU cc_start: 0.7992 (pt0) cc_final: 0.7734 (pt0) REVERT: A 35 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8811 (ttmt) REVERT: A 186 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 232 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7934 (mp) REVERT: A 285 ILE cc_start: 0.8116 (mm) cc_final: 0.7888 (mt) REVERT: B 22 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.4686 (mpt-90) REVERT: B 227 SER cc_start: 0.9419 (m) cc_final: 0.9115 (t) REVERT: B 234 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8824 (t80) REVERT: B 258 ASP cc_start: 0.8136 (t70) cc_final: 0.7468 (t0) REVERT: C 52 THR cc_start: 0.7758 (m) cc_final: 0.7377 (p) outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 1.2821 time to fit residues: 185.3171 Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8743 Z= 0.247 Angle : 0.591 7.803 11915 Z= 0.312 Chirality : 0.044 0.144 1388 Planarity : 0.004 0.053 1514 Dihedral : 4.312 18.812 1240 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.44 % Allowed : 23.04 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.16 (0.25), residues: 1141 helix: 2.73 (0.26), residues: 403 sheet: 0.77 (0.30), residues: 277 loop : -1.08 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.002 PHE R 241 TYR 0.019 0.002 TYR R 25 ARG 0.007 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.982 Fit side-chains REVERT: A 20 ASP cc_start: 0.8614 (m-30) cc_final: 0.8321 (m-30) REVERT: A 35 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8891 (ttmt) REVERT: A 186 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 232 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 285 ILE cc_start: 0.8220 (mm) cc_final: 0.7973 (mt) REVERT: B 22 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.5194 (mpt-90) REVERT: B 217 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8056 (pmt) REVERT: B 227 SER cc_start: 0.9434 (m) cc_final: 0.9110 (t) REVERT: B 234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8763 (t80) outliers start: 29 outliers final: 14 residues processed: 134 average time/residue: 1.2341 time to fit residues: 176.7398 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR 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 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.188 Angle : 0.542 6.847 11915 Z= 0.289 Chirality : 0.042 0.141 1388 Planarity : 0.004 0.053 1514 Dihedral : 4.161 18.301 1240 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.21 % Allowed : 23.04 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.25), residues: 1141 helix: 2.83 (0.26), residues: 403 sheet: 0.79 (0.30), residues: 277 loop : -1.03 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR S 190 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.969 Fit side-chains REVERT: A 35 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8858 (ttmt) REVERT: A 232 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 285 ILE cc_start: 0.8289 (mm) cc_final: 0.8026 (mt) REVERT: B 22 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5164 (mpt-90) REVERT: B 217 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8104 (pmt) REVERT: B 227 SER cc_start: 0.9404 (m) cc_final: 0.9103 (t) REVERT: B 234 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8687 (t80) REVERT: R 214 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7283 (mp) outliers start: 27 outliers final: 14 residues processed: 142 average time/residue: 1.2219 time to fit residues: 185.0284 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR 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 C residue 54 VAL Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8743 Z= 0.308 Angle : 0.633 8.891 11915 Z= 0.334 Chirality : 0.045 0.156 1388 Planarity : 0.004 0.055 1514 Dihedral : 4.475 21.135 1240 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.80 % Allowed : 22.45 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1141 helix: 2.59 (0.26), residues: 406 sheet: 0.67 (0.30), residues: 280 loop : -1.15 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.024 0.002 PHE R 34 TYR 0.021 0.002 TYR R 25 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.963 Fit side-chains REVERT: A 20 ASP cc_start: 0.8621 (m-30) cc_final: 0.8339 (m-30) REVERT: A 285 ILE cc_start: 0.8404 (mm) cc_final: 0.8123 (mt) REVERT: B 217 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8039 (pmt) REVERT: B 227 SER cc_start: 0.9414 (m) cc_final: 0.9089 (t) REVERT: B 234 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8764 (t80) REVERT: R 214 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7480 (mp) outliers start: 32 outliers final: 12 residues processed: 135 average time/residue: 1.1622 time to fit residues: 167.9548 Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 181 THR 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 C residue 54 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.177 Angle : 0.547 9.409 11915 Z= 0.290 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.053 1514 Dihedral : 4.203 18.681 1240 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 24.47 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.25), residues: 1141 helix: 2.81 (0.26), residues: 405 sheet: 0.80 (0.30), residues: 282 loop : -1.04 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE R 34 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.998 Fit side-chains REVERT: B 217 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8096 (pmt) REVERT: B 227 SER cc_start: 0.9394 (m) cc_final: 0.9091 (t) REVERT: B 234 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8717 (t80) REVERT: R 214 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7387 (mp) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 1.3154 time to fit residues: 185.0531 Evaluate side-chains 123 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 181 THR 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 C residue 54 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8743 Z= 0.199 Angle : 0.567 10.522 11915 Z= 0.298 Chirality : 0.043 0.142 1388 Planarity : 0.004 0.053 1514 Dihedral : 4.170 18.538 1240 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 24.94 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.28 (0.25), residues: 1141 helix: 2.82 (0.26), residues: 405 sheet: 0.81 (0.30), residues: 282 loop : -1.03 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.023 0.001 PHE R 34 TYR 0.020 0.001 TYR R 25 ARG 0.006 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.034 Fit side-chains REVERT: B 217 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8073 (pmt) REVERT: B 227 SER cc_start: 0.9401 (m) cc_final: 0.9091 (t) REVERT: B 234 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8695 (t80) REVERT: R 214 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7351 (mp) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 1.1767 time to fit residues: 152.5057 Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR 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 C residue 54 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108426 restraints weight = 10702.028| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.25 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8743 Z= 0.173 Angle : 0.550 13.151 11915 Z= 0.287 Chirality : 0.042 0.143 1388 Planarity : 0.004 0.052 1514 Dihedral : 4.073 18.247 1240 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.14 % Allowed : 24.58 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.32 (0.25), residues: 1141 helix: 2.89 (0.26), residues: 405 sheet: 0.79 (0.30), residues: 286 loop : -1.02 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.023 0.001 PHE R 34 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.79 seconds wall clock time: 66 minutes 15.54 seconds (3975.54 seconds total)