Starting phenix.real_space_refine on Tue Sep 24 04:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/09_2024/6ddf_7869_neut.cif" } resolution = 3.5 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= 0.021 sd= 0.567 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 4342 2.51 5 N 1165 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6808 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1694 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 396 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2134 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.67 Number of scatterers: 6808 At special positions: 0 Unit cell: (76.96, 118.56, 112.32, 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 1249 8.00 N 1165 7.00 C 4342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 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=1, symmetry=0 Links applied TRANS " DAL D 2 " - " TYR D 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 4.094A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.560A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.545A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 5.163A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.834A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.720A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.601A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.323A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 removed outlier: 3.672A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 97 removed outlier: 3.768A pdb=" N LEU R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.999A pdb=" N ILE R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 130 removed outlier: 3.627A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN R 127 " --> pdb=" O PHE R 123 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 171 removed outlier: 3.795A pdb=" N CYS R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 182 through 204 removed outlier: 3.612A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 229 through 241 removed outlier: 3.956A pdb=" N LYS R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 249 Processing helix chain 'R' and resid 249 through 260 removed outlier: 4.254A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 294 Processing helix chain 'R' and resid 294 through 306 removed outlier: 3.826A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 326 removed outlier: 4.027A pdb=" N SER R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 336 Proline residue: R 333 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.911A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 6.664A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.594A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.617A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.613A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.895A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.629A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.436A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.671A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 849 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: 1.79 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1369 1.33 - 1.45: 1720 1.45 - 1.58: 3779 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 6943 Sorted by residual: bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.24e-02 6.50e+03 7.30e+00 bond pdb=" O ETA D 5 " pdb=" CB ETA D 5 " ideal model delta sigma weight residual 1.413 1.459 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.35e-02 5.49e+03 4.34e+00 bond pdb=" CB PRO R 244 " pdb=" CG PRO R 244 " ideal model delta sigma weight residual 1.492 1.392 0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.22e-02 6.72e+03 2.88e+00 ... (remaining 6938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9027 2.19 - 4.39: 331 4.39 - 6.58: 46 6.58 - 8.77: 15 8.77 - 10.97: 8 Bond angle restraints: 9427 Sorted by residual: angle pdb=" N LEU R 121 " pdb=" CA LEU R 121 " pdb=" C LEU R 121 " ideal model delta sigma weight residual 109.81 120.78 -10.97 2.21e+00 2.05e-01 2.46e+01 angle pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N MEA D 4 " pdb=" CA MEA D 4 " pdb=" CB MEA D 4 " ideal model delta sigma weight residual 110.50 117.47 -6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C ASP B 27 " pdb=" N ALA B 28 " pdb=" CA ALA B 28 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 108.96 103.24 5.72 1.59e+00 3.96e-01 1.29e+01 ... (remaining 9422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.19: 3677 12.19 - 24.39: 324 24.39 - 36.58: 74 36.58 - 48.78: 27 48.78 - 60.97: 1 Dihedral angle restraints: 4103 sinusoidal: 1503 harmonic: 2600 Sorted by residual: dihedral pdb=" CA ILE A 49 " pdb=" C ILE A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA SER R 214 " pdb=" C SER R 214 " pdb=" N ILE R 215 " pdb=" CA ILE R 215 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 151.90 28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 4100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 796 0.057 - 0.113: 251 0.113 - 0.170: 41 0.170 - 0.227: 7 0.227 - 0.284: 3 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA LEU R 121 " pdb=" N LEU R 121 " pdb=" C LEU R 121 " pdb=" CB LEU R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 37 " pdb=" CA ILE B 37 " pdb=" CG1 ILE B 37 " pdb=" CG2 ILE B 37 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1095 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.66e-02 6.88e+00 pdb=" CG TRP B 63 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 49 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 180 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO R 181 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.032 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1188 2.76 - 3.30: 6364 3.30 - 3.83: 11292 3.83 - 4.37: 12756 4.37 - 4.90: 22133 Nonbonded interactions: 53733 Sorted by model distance: nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 246 " model vdw 2.228 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.310 3.040 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.313 3.120 ... (remaining 53728 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 6943 Z= 0.399 Angle : 1.014 10.968 9427 Z= 0.540 Chirality : 0.057 0.284 1098 Planarity : 0.007 0.065 1189 Dihedral : 10.482 60.972 2411 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.34 % Favored : 91.54 % Rotamer: Outliers : 0.72 % Allowed : 5.15 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.62 (0.23), residues: 875 helix: -2.94 (0.19), residues: 347 sheet: -3.53 (0.36), residues: 159 loop : -2.74 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 63 HIS 0.011 0.002 HIS B 183 PHE 0.031 0.003 PHE B 241 TYR 0.031 0.003 TYR R 299 ARG 0.004 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7114 (t70) cc_final: 0.6641 (t0) REVERT: B 65 THR cc_start: 0.7469 (p) cc_final: 0.7212 (p) REVERT: B 78 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7742 (mmtt) REVERT: B 123 ILE cc_start: 0.8588 (pp) cc_final: 0.8376 (pt) REVERT: R 162 SER cc_start: 0.8137 (t) cc_final: 0.7889 (t) REVERT: R 198 ILE cc_start: 0.3926 (tp) cc_final: 0.3041 (mt) REVERT: R 216 ASP cc_start: 0.7316 (t0) cc_final: 0.6711 (t0) REVERT: R 336 TYR cc_start: 0.7601 (m-10) cc_final: 0.7219 (m-80) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.1748 time to fit residues: 55.2238 Evaluate side-chains 161 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 HIS A 269 ASN A 294 ASN B 13 GLN B 88 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS ** R 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6943 Z= 0.202 Angle : 0.673 9.027 9427 Z= 0.345 Chirality : 0.042 0.135 1098 Planarity : 0.005 0.044 1189 Dihedral : 6.057 64.944 959 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.72 % Allowed : 15.31 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.22 (0.26), residues: 875 helix: -1.12 (0.25), residues: 341 sheet: -3.17 (0.36), residues: 161 loop : -2.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE B 151 TYR 0.015 0.001 TYR R 149 ARG 0.006 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8374 (pt) REVERT: B 234 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: C 32 LYS cc_start: 0.7713 (tppt) cc_final: 0.7364 (mttm) REVERT: R 324 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6832 (pt) outliers start: 26 outliers final: 17 residues processed: 214 average time/residue: 0.1926 time to fit residues: 53.4033 Evaluate side-chains 179 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0370 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 13 GLN B 32 GLN B 119 ASN C 44 HIS R 274 ASN R 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6943 Z= 0.162 Angle : 0.642 9.610 9427 Z= 0.323 Chirality : 0.042 0.131 1098 Planarity : 0.004 0.037 1189 Dihedral : 5.553 65.165 959 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.43 % Allowed : 19.46 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.63 (0.28), residues: 875 helix: -0.42 (0.27), residues: 349 sheet: -2.97 (0.38), residues: 152 loop : -2.43 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.006 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.6883 (mm110) cc_final: 0.6521 (mm110) REVERT: B 123 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8114 (pt) REVERT: B 200 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (m) REVERT: B 234 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: B 297 TRP cc_start: 0.8201 (m100) cc_final: 0.7991 (m100) REVERT: C 18 GLN cc_start: 0.7688 (tp40) cc_final: 0.7387 (tp40) REVERT: R 293 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.6919 (m-10) outliers start: 31 outliers final: 15 residues processed: 202 average time/residue: 0.1916 time to fit residues: 50.6846 Evaluate side-chains 181 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6943 Z= 0.214 Angle : 0.643 9.164 9427 Z= 0.329 Chirality : 0.042 0.124 1098 Planarity : 0.004 0.036 1189 Dihedral : 5.415 61.567 959 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.58 % Allowed : 19.89 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.27 (0.29), residues: 875 helix: -0.16 (0.27), residues: 352 sheet: -2.80 (0.37), residues: 156 loop : -2.17 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.024 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.004 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7374 (mmp) cc_final: 0.7070 (mmp) REVERT: B 78 LYS cc_start: 0.8362 (mmpt) cc_final: 0.8110 (mmtm) REVERT: B 164 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7349 (p) REVERT: B 234 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: C 18 GLN cc_start: 0.7685 (tp40) cc_final: 0.7371 (tp40) REVERT: R 98 LYS cc_start: 0.6491 (mmtt) cc_final: 0.5907 (mmmt) REVERT: R 293 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.6931 (m-10) outliers start: 39 outliers final: 23 residues processed: 199 average time/residue: 0.1885 time to fit residues: 49.1933 Evaluate side-chains 184 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 213 HIS B 13 GLN B 110 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6943 Z= 0.304 Angle : 0.688 8.935 9427 Z= 0.350 Chirality : 0.044 0.148 1098 Planarity : 0.004 0.042 1189 Dihedral : 5.545 57.888 959 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.72 % Allowed : 21.89 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.19 (0.29), residues: 875 helix: -0.13 (0.28), residues: 351 sheet: -2.65 (0.37), residues: 156 loop : -2.15 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.028 0.002 PHE B 222 TYR 0.014 0.002 TYR R 149 ARG 0.011 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7752 (tt0) cc_final: 0.7423 (tt0) REVERT: B 118 ASP cc_start: 0.7078 (p0) cc_final: 0.6676 (p0) REVERT: B 234 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: C 18 GLN cc_start: 0.7596 (tp40) cc_final: 0.7333 (tp40) REVERT: R 293 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6860 (m-10) outliers start: 40 outliers final: 26 residues processed: 190 average time/residue: 0.2133 time to fit residues: 53.0763 Evaluate side-chains 180 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6943 Z= 0.204 Angle : 0.663 13.620 9427 Z= 0.333 Chirality : 0.044 0.285 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.387 63.849 959 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.15 % Allowed : 22.75 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.97 (0.29), residues: 875 helix: 0.05 (0.28), residues: 349 sheet: -2.45 (0.38), residues: 156 loop : -2.05 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.026 0.001 PHE B 222 TYR 0.015 0.001 TYR R 149 ARG 0.007 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7686 (tt0) cc_final: 0.7398 (tt0) REVERT: A 310 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 75 GLN cc_start: 0.7252 (mm110) cc_final: 0.6662 (mm110) REVERT: B 78 LYS cc_start: 0.8357 (mmpt) cc_final: 0.7634 (mmtm) REVERT: B 164 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7283 (p) REVERT: B 234 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: R 83 LEU cc_start: 0.6529 (tm) cc_final: 0.6321 (tp) REVERT: R 293 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.6674 (m-10) outliers start: 36 outliers final: 24 residues processed: 180 average time/residue: 0.1827 time to fit residues: 43.7446 Evaluate side-chains 172 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6943 Z= 0.204 Angle : 0.665 16.883 9427 Z= 0.332 Chirality : 0.044 0.250 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.250 63.943 957 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.86 % Allowed : 23.75 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.80 (0.29), residues: 875 helix: 0.20 (0.28), residues: 349 sheet: -2.22 (0.39), residues: 155 loop : -2.04 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.027 0.001 PHE B 222 TYR 0.015 0.001 TYR R 149 ARG 0.006 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7676 (tt0) cc_final: 0.7394 (tt0) REVERT: A 310 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8361 (tp) REVERT: B 78 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7566 (mmtm) REVERT: B 164 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7246 (p) REVERT: B 234 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: R 293 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.6540 (m-10) outliers start: 34 outliers final: 24 residues processed: 181 average time/residue: 0.1935 time to fit residues: 46.2176 Evaluate side-chains 168 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 13 GLN B 220 GLN C 18 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6943 Z= 0.187 Angle : 0.646 10.832 9427 Z= 0.325 Chirality : 0.043 0.162 1098 Planarity : 0.004 0.035 1189 Dihedral : 5.157 65.805 957 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.15 % Allowed : 24.75 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.57 (0.30), residues: 875 helix: 0.36 (0.28), residues: 350 sheet: -1.96 (0.41), residues: 151 loop : -1.96 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.002 0.001 HIS B 142 PHE 0.027 0.001 PHE B 222 TYR 0.016 0.001 TYR R 149 ARG 0.006 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7673 (tt0) cc_final: 0.7270 (tt0) REVERT: B 78 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7561 (mmtm) REVERT: B 164 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7323 (p) REVERT: B 234 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: R 293 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6855 (m-10) outliers start: 36 outliers final: 29 residues processed: 177 average time/residue: 0.1973 time to fit residues: 45.9893 Evaluate side-chains 176 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6943 Z= 0.209 Angle : 0.654 9.141 9427 Z= 0.330 Chirality : 0.043 0.170 1098 Planarity : 0.004 0.034 1189 Dihedral : 5.159 64.619 957 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.15 % Allowed : 24.32 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.52 (0.30), residues: 875 helix: 0.42 (0.28), residues: 350 sheet: -2.01 (0.41), residues: 145 loop : -1.93 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.030 0.001 PHE B 222 TYR 0.016 0.001 TYR R 149 ARG 0.006 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7620 (tt0) cc_final: 0.7280 (tt0) REVERT: A 310 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8389 (tp) REVERT: B 78 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7566 (mmtm) REVERT: B 118 ASP cc_start: 0.7023 (p0) cc_final: 0.6813 (p0) REVERT: B 164 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7249 (p) REVERT: B 234 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: R 293 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6865 (m-10) outliers start: 36 outliers final: 29 residues processed: 172 average time/residue: 0.1916 time to fit residues: 43.2749 Evaluate side-chains 171 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6943 Z= 0.244 Angle : 0.678 8.731 9427 Z= 0.345 Chirality : 0.044 0.179 1098 Planarity : 0.004 0.054 1189 Dihedral : 5.234 62.018 957 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.15 % Allowed : 24.46 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.30), residues: 875 helix: 0.28 (0.28), residues: 350 sheet: -1.97 (0.41), residues: 146 loop : -1.81 (0.35), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 339 HIS 0.002 0.001 HIS R 171 PHE 0.021 0.002 PHE B 222 TYR 0.015 0.002 TYR R 149 ARG 0.008 0.001 ARG R 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7533 (tt0) cc_final: 0.7271 (tt0) REVERT: B 78 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7582 (mmtm) REVERT: B 234 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: R 293 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.6864 (m-10) outliers start: 36 outliers final: 28 residues processed: 170 average time/residue: 0.1894 time to fit residues: 42.5088 Evaluate side-chains 173 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS C 18 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133033 restraints weight = 11132.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136913 restraints weight = 6009.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139550 restraints weight = 3807.890| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6943 Z= 0.197 Angle : 0.661 9.502 9427 Z= 0.333 Chirality : 0.043 0.169 1098 Planarity : 0.004 0.044 1189 Dihedral : 5.165 66.981 957 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.29 % Allowed : 25.46 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.46 (0.29), residues: 875 helix: 0.41 (0.28), residues: 350 sheet: -1.87 (0.42), residues: 149 loop : -1.88 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.002 0.000 HIS R 171 PHE 0.024 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.009 0.001 ARG R 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.59 seconds wall clock time: 35 minutes 3.93 seconds (2103.93 seconds total)