Starting phenix.real_space_refine on Mon Mar 11 08:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcb_37437/03_2024/8wcb_37437_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.189 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 49 5.16 5 C 4953 2.51 5 N 1346 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "Y GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1686 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 6 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2354 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 93 Chain: "R" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1719 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain breaks: 12 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1681 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "Y" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 337 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HAI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.76 Number of scatterers: 7784 At special positions: 0 Unit cell: (80.96, 118.68, 121.44, 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 49 16.00 O 1436 8.00 N 1346 7.00 C 4953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 29.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 4.158A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.910A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 4.037A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.706A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.619A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'R' and resid 24 through 45 removed outlier: 4.317A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 82 removed outlier: 4.013A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N CYS R 73 " --> pdb=" O ASP R 68 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU R 74 " --> pdb=" O PHE R 69 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE R 75 " --> pdb=" O LEU R 70 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 92 through 121 removed outlier: 4.492A pdb=" N LYS R 96 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE R 103 " --> pdb=" O SER R 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA R 108 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 111 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 156 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 175 through 178 No H-bonds generated for 'chain 'R' and resid 175 through 178' Processing helix chain 'R' and resid 187 through 193 removed outlier: 3.755A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 219 Processing helix chain 'R' and resid 246 through 272 removed outlier: 3.632A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 4.983A pdb=" N LEU R 270 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP R 271 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 283 No H-bonds generated for 'chain 'R' and resid 280 through 283' Processing helix chain 'R' and resid 291 through 303 Proline residue: R 298 - end of helix removed outlier: 3.509A pdb=" N PHE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 308 No H-bonds generated for 'chain 'R' and resid 306 through 308' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'Y' and resid 11 through 23 Processing helix chain 'Y' and resid 30 through 33 No H-bonds generated for 'chain 'Y' and resid 30 through 33' Processing helix chain 'Y' and resid 35 through 43 removed outlier: 3.727A pdb=" N ALA Y 43 " --> pdb=" O TYR Y 40 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.652A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.784A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.727A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.941A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.618A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 307 through 309 removed outlier: 5.048A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.926A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.519A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 174 through 176 Processing sheet with id= M, first strand: chain 'S' and resid 225 through 227 314 hydrogen bonds defined for protein. 828 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: 2.73 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.50: 4776 1.50 - 1.84: 3161 1.84 - 2.19: 0 2.19 - 2.53: 0 2.53 - 2.87: 1 Bond restraints: 7938 Sorted by residual: bond pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 1.331 2.874 -1.543 1.33e-02 5.65e+03 1.35e+04 bond pdb=" C LEU R 286 " pdb=" N TYR R 287 " ideal model delta sigma weight residual 1.329 1.474 -0.145 1.40e-02 5.10e+03 1.07e+02 bond pdb=" CA ILE R 110 " pdb=" C ILE R 110 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.18e-02 7.18e+03 4.48e+01 bond pdb=" C ILE S 189 " pdb=" O ILE S 189 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C THR R 101 " pdb=" O THR R 101 " ideal model delta sigma weight residual 1.237 1.163 0.073 1.16e-02 7.43e+03 3.98e+01 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 81.76 - 98.95: 3 98.95 - 116.13: 5208 116.13 - 133.32: 5563 133.32 - 150.51: 24 150.51 - 167.69: 1 Bond angle restraints: 10799 Sorted by residual: angle pdb=" O ALA B 309 " pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 122.89 81.76 41.13 1.22e+00 6.72e-01 1.14e+03 angle pdb=" C ALA B 309 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 122.36 167.69 -45.33 1.60e+00 3.91e-01 8.03e+02 angle pdb=" CA ALA B 309 " pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 115.88 131.92 -16.04 1.28e+00 6.10e-01 1.57e+02 angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.89 100.42 12.47 1.24e+00 6.50e-01 1.01e+02 angle pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" C LYS R 51 " ideal model delta sigma weight residual 114.39 100.50 13.89 1.45e+00 4.76e-01 9.18e+01 ... (remaining 10794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 4119 14.59 - 29.18: 375 29.18 - 43.77: 106 43.77 - 58.36: 17 58.36 - 72.96: 9 Dihedral angle restraints: 4626 sinusoidal: 1531 harmonic: 3095 Sorted by residual: dihedral pdb=" N ASP R 102 " pdb=" C ASP R 102 " pdb=" CA ASP R 102 " pdb=" CB ASP R 102 " ideal model delta harmonic sigma weight residual 122.80 137.53 -14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" C ASP R 102 " pdb=" N ASP R 102 " pdb=" CA ASP R 102 " pdb=" CB ASP R 102 " ideal model delta harmonic sigma weight residual -122.60 -136.61 14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C SER R 48 " pdb=" N SER R 48 " pdb=" CA SER R 48 " pdb=" CB SER R 48 " ideal model delta harmonic sigma weight residual -122.60 -134.77 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 4623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1200 0.135 - 0.271: 40 0.271 - 0.406: 14 0.406 - 0.541: 2 0.541 - 0.676: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ASP R 102 " pdb=" N ASP R 102 " pdb=" C ASP R 102 " pdb=" CB ASP R 102 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CA SER R 48 " pdb=" N SER R 48 " pdb=" C SER R 48 " pdb=" CB SER R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 1254 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 309 " 0.155 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C ALA B 309 " -0.338 2.00e-02 2.50e+03 pdb=" O ALA B 309 " 0.128 2.00e-02 2.50e+03 pdb=" N HIS B 311 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 286 " 0.025 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C LEU R 286 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU R 286 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR R 287 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 279 " 0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO R 280 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO R 280 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO R 280 " 0.053 5.00e-02 4.00e+02 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1719 2.78 - 3.31: 7283 3.31 - 3.84: 13069 3.84 - 4.37: 15428 4.37 - 4.90: 26623 Nonbonded interactions: 64122 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.246 2.440 nonbonded pdb=" N ARG S 38 " pdb=" O GLU S 46 " model vdw 2.271 2.520 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.277 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.295 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.296 2.440 ... (remaining 64117 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.730 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.020 Find NCS groups from input model: 0.270 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:2.680 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 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 : 0.019 1.543 7938 Z= 1.417 Angle : 1.204 45.333 10799 Z= 0.800 Chirality : 0.070 0.676 1257 Planarity : 0.009 0.199 1372 Dihedral : 12.909 72.956 2608 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.09 % Allowed : 1.64 % Favored : 97.27 % Cbeta Deviations : 0.40 % 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: -0.88 (0.27), residues: 1016 helix: 0.04 (0.30), residues: 318 sheet: -0.22 (0.34), residues: 244 loop : -1.16 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 277 HIS 0.010 0.002 HIS A 357 PHE 0.021 0.002 PHE R 184 TYR 0.029 0.001 TYR R 301 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.7677 (tptt) cc_final: 0.7443 (mmtt) REVERT: R 276 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 8 outliers final: 3 residues processed: 147 average time/residue: 0.2132 time to fit residues: 41.6897 Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 305 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7938 Z= 0.213 Angle : 0.554 6.493 10799 Z= 0.293 Chirality : 0.042 0.161 1257 Planarity : 0.005 0.065 1372 Dihedral : 5.182 59.692 1142 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.05 % Allowed : 7.78 % Favored : 90.18 % 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: -0.38 (0.27), residues: 1018 helix: 0.60 (0.31), residues: 310 sheet: 0.03 (0.34), residues: 247 loop : -0.94 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE R 184 TYR 0.012 0.001 TYR R 210 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.905 Fit side-chains REVERT: A 239 ASN cc_start: 0.6844 (t0) cc_final: 0.6618 (t0) REVERT: R 276 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7109 (m-80) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.1857 time to fit residues: 35.4532 Evaluate side-chains 131 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 271 ASN B 259 GLN S 179 GLN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7938 Z= 0.218 Angle : 0.533 6.287 10799 Z= 0.281 Chirality : 0.042 0.231 1257 Planarity : 0.004 0.053 1372 Dihedral : 4.964 59.084 1139 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.91 % Allowed : 12.01 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1018 helix: 0.89 (0.31), residues: 308 sheet: -0.05 (0.33), residues: 256 loop : -0.84 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 184 TYR 0.015 0.001 TYR B 85 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.6390 (m110) cc_final: 0.5913 (m110) REVERT: R 276 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7025 (m-80) outliers start: 14 outliers final: 11 residues processed: 130 average time/residue: 0.1914 time to fit residues: 34.2392 Evaluate side-chains 123 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 237 ASN B 239 ASN R 40 ASN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7938 Z= 0.199 Angle : 0.520 6.611 10799 Z= 0.272 Chirality : 0.042 0.178 1257 Planarity : 0.004 0.046 1372 Dihedral : 4.937 59.728 1139 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 13.23 % Favored : 84.04 % 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: -0.06 (0.27), residues: 1018 helix: 1.07 (0.31), residues: 308 sheet: 0.08 (0.33), residues: 254 loop : -0.83 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.020 0.001 TYR B 85 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.759 Fit side-chains REVERT: R 276 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6951 (m-80) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 0.1828 time to fit residues: 32.6118 Evaluate side-chains 126 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7938 Z= 0.239 Angle : 0.547 6.609 10799 Z= 0.286 Chirality : 0.042 0.163 1257 Planarity : 0.004 0.043 1372 Dihedral : 4.945 53.259 1139 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.73 % Allowed : 15.42 % Favored : 81.86 % 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: -0.04 (0.27), residues: 1018 helix: 1.18 (0.31), residues: 301 sheet: -0.16 (0.32), residues: 274 loop : -0.70 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.021 0.002 TYR B 85 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.903 Fit side-chains REVERT: R 276 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6885 (m-80) outliers start: 20 outliers final: 15 residues processed: 124 average time/residue: 0.1769 time to fit residues: 31.1320 Evaluate side-chains 129 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 293 ASN Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7938 Z= 0.207 Angle : 0.526 6.888 10799 Z= 0.274 Chirality : 0.042 0.206 1257 Planarity : 0.004 0.038 1372 Dihedral : 4.762 49.290 1139 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.27 % Allowed : 16.23 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1018 helix: 1.23 (0.31), residues: 302 sheet: -0.02 (0.33), residues: 261 loop : -0.79 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 332 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.017 0.001 TYR B 85 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.833 Fit side-chains REVERT: B 332 TRP cc_start: 0.8003 (m-10) cc_final: 0.7768 (m-10) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.1777 time to fit residues: 32.1092 Evaluate side-chains 130 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7938 Z= 0.204 Angle : 0.521 7.050 10799 Z= 0.271 Chirality : 0.041 0.139 1257 Planarity : 0.004 0.037 1372 Dihedral : 4.515 48.969 1137 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.27 % Allowed : 16.64 % Favored : 80.08 % 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: -0.00 (0.27), residues: 1018 helix: 1.16 (0.31), residues: 307 sheet: -0.02 (0.33), residues: 266 loop : -0.75 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 273 TYR 0.016 0.001 TYR B 85 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.906 Fit side-chains REVERT: A 271 ASN cc_start: 0.6355 (m-40) cc_final: 0.6099 (m-40) REVERT: B 332 TRP cc_start: 0.8006 (m-10) cc_final: 0.7747 (m-10) REVERT: S 219 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 24 outliers final: 19 residues processed: 124 average time/residue: 0.1752 time to fit residues: 30.7267 Evaluate side-chains 128 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 0.0970 chunk 68 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7938 Z= 0.149 Angle : 0.494 7.226 10799 Z= 0.256 Chirality : 0.041 0.243 1257 Planarity : 0.003 0.039 1372 Dihedral : 4.274 51.422 1137 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.59 % Allowed : 17.60 % Favored : 79.81 % 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: 0.07 (0.27), residues: 1018 helix: 1.25 (0.31), residues: 307 sheet: 0.06 (0.33), residues: 262 loop : -0.75 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 273 TYR 0.011 0.001 TYR B 85 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.863 Fit side-chains REVERT: B 332 TRP cc_start: 0.7991 (m-10) cc_final: 0.7740 (m-10) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.1891 time to fit residues: 33.5253 Evaluate side-chains 127 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7938 Z= 0.227 Angle : 0.537 7.404 10799 Z= 0.276 Chirality : 0.042 0.137 1257 Planarity : 0.004 0.039 1372 Dihedral : 4.473 49.229 1137 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.59 % Allowed : 17.46 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 1018 helix: 1.20 (0.31), residues: 307 sheet: 0.03 (0.33), residues: 265 loop : -0.73 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.018 0.001 TYR B 85 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.923 Fit side-chains REVERT: B 105 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7431 (t80) REVERT: B 332 TRP cc_start: 0.8026 (m-10) cc_final: 0.7792 (m-10) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.1742 time to fit residues: 28.8922 Evaluate side-chains 124 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 0.0000 chunk 96 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7938 Z= 0.184 Angle : 0.514 7.520 10799 Z= 0.266 Chirality : 0.042 0.228 1257 Planarity : 0.003 0.039 1372 Dihedral : 4.361 50.835 1137 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.91 % Allowed : 18.28 % Favored : 79.81 % 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: 0.07 (0.27), residues: 1018 helix: 1.24 (0.31), residues: 307 sheet: 0.03 (0.33), residues: 264 loop : -0.72 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.001 PHE R 273 TYR 0.014 0.001 TYR B 85 ARG 0.007 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.879 Fit side-chains REVERT: A 299 GLU cc_start: 0.6876 (mp0) cc_final: 0.6664 (mp0) REVERT: B 332 TRP cc_start: 0.7987 (m-10) cc_final: 0.7744 (m-10) REVERT: R 286 LEU cc_start: 0.6471 (mp) cc_final: 0.6000 (mt) outliers start: 14 outliers final: 14 residues processed: 122 average time/residue: 0.1761 time to fit residues: 29.9600 Evaluate side-chains 123 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.191859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155838 restraints weight = 8606.732| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.11 r_work: 0.3779 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7938 Z= 0.259 Angle : 0.555 7.565 10799 Z= 0.288 Chirality : 0.042 0.142 1257 Planarity : 0.004 0.039 1372 Dihedral : 4.597 49.009 1137 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.59 % Allowed : 17.60 % Favored : 79.81 % 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: -0.09 (0.27), residues: 1018 helix: 1.13 (0.31), residues: 307 sheet: -0.28 (0.31), residues: 285 loop : -0.69 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.021 0.002 TYR B 85 ARG 0.007 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.41 seconds wall clock time: 37 minutes 22.67 seconds (2242.67 seconds total)