Starting phenix.real_space_refine on Tue Feb 13 17:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy6_33512/02_2024/7xy6_33512_updated.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 48 5.16 5 C 4481 2.51 5 N 1229 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7044 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1851 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2239 Unusual residues: {'I5D': 1} Classifications: {'peptide': 286, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 274, None: 1} Not linked: pdbres="TYR R 308 " pdbres="I5D R 501 " Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.32, per 1000 atoms: 0.61 Number of scatterers: 7044 At special positions: 0 Unit cell: (85.44, 101.76, 133.44, 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 48 16.00 O 1286 8.00 N 1229 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 41.3% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.795A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 315 through 334 removed outlier: 3.511A pdb=" N ILE A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 removed outlier: 3.870A pdb=" N ILE A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.792A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.712A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 5 through 33 Processing helix chain 'R' and resid 41 through 69 removed outlier: 4.180A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 75 through 108 removed outlier: 3.784A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA R 82 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR R 89 " --> pdb=" O VAL R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 116 No H-bonds generated for 'chain 'R' and resid 113 through 116' Processing helix chain 'R' and resid 119 through 137 Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 173 through 175 No H-bonds generated for 'chain 'R' and resid 173 through 175' Processing helix chain 'R' and resid 179 through 184 Processing helix chain 'R' and resid 187 through 190 No H-bonds generated for 'chain 'R' and resid 187 through 190' Processing helix chain 'R' and resid 192 through 217 Processing helix chain 'R' and resid 224 through 259 removed outlier: 4.169A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Proline residue: R 249 - end of helix removed outlier: 3.600A pdb=" N VAL R 253 " --> pdb=" O PRO R 249 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS R 255 " --> pdb=" O HIS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 265 No H-bonds generated for 'chain 'R' and resid 262 through 265' Processing helix chain 'R' and resid 270 through 290 removed outlier: 3.658A pdb=" N ALA R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN R 286 " --> pdb=" O ASN R 282 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 295 through 307 Processing sheet with id= A, first strand: chain 'A' and resid 342 through 346 removed outlier: 7.504A pdb=" N VAL A 270 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N HIS A 345 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 272 " --> pdb=" O HIS A 345 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 236 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 34 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 205 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.018A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.389A 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: 6.802A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.731A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.056A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.961A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.654A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.648A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 918 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: 2.06 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1146 1.26 - 1.40: 1821 1.40 - 1.54: 4141 1.54 - 1.68: 12 1.68 - 1.82: 67 Bond restraints: 7187 Sorted by residual: bond pdb=" C4' I5D R 501 " pdb=" C5' I5D R 501 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C16 I5D R 501 " pdb=" C17 I5D R 501 " ideal model delta sigma weight residual 1.391 1.525 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C10 I5D R 501 " pdb=" C11 I5D R 501 " ideal model delta sigma weight residual 1.391 1.521 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C11 I5D R 501 " pdb=" C16 I5D R 501 " ideal model delta sigma weight residual 1.391 1.314 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C17 I5D R 501 " pdb=" C4' I5D R 501 " ideal model delta sigma weight residual 1.391 1.315 0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 7182 not shown) Histogram of bond angle deviations from ideal: 59.52 - 83.52: 3 83.52 - 107.51: 211 107.51 - 131.51: 9516 131.51 - 155.50: 15 155.50 - 179.50: 2 Bond angle restraints: 9747 Sorted by residual: angle pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" CD PRO A 296 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 angle pdb=" N LEU A 376 " pdb=" CA LEU A 376 " pdb=" C LEU A 376 " ideal model delta sigma weight residual 114.04 109.95 4.09 1.24e+00 6.50e-01 1.09e+01 angle pdb=" N9 I5D R 501 " pdb=" C8 I5D R 501 " pdb=" NAA I5D R 501 " ideal model delta sigma weight residual 112.13 120.83 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" C10 I5D R 501 " pdb=" C11 I5D R 501 " pdb=" OP3 I5D R 501 " ideal model delta sigma weight residual 112.38 120.17 -7.79 3.00e+00 1.11e-01 6.75e+00 angle pdb=" CA SER R 279 " pdb=" C SER R 279 " pdb=" O SER R 279 " ideal model delta sigma weight residual 120.55 117.94 2.61 1.06e+00 8.90e-01 6.06e+00 ... (remaining 9742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3767 18.05 - 36.10: 401 36.10 - 54.14: 77 54.14 - 72.19: 17 72.19 - 90.24: 9 Dihedral angle restraints: 4271 sinusoidal: 1660 harmonic: 2611 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 171 " pdb=" CB CYS R 171 " ideal model delta sinusoidal sigma weight residual 93.00 159.70 -66.70 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" N1 I5D R 501 " pdb=" C5 I5D R 501 " pdb=" C6 I5D R 501 " pdb=" S1 I5D R 501 " ideal model delta sinusoidal sigma weight residual 172.38 -97.38 -90.24 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA CYS R 171 " pdb=" C CYS R 171 " pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 668 0.027 - 0.055: 259 0.055 - 0.082: 113 0.082 - 0.110: 53 0.110 - 0.137: 20 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1110 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 I5D R 501 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C6 I5D R 501 " -0.093 2.00e-02 2.50e+03 pdb=" N1 I5D R 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 I5D R 501 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 295 " 0.042 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 296 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO G 49 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.028 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1066 2.76 - 3.29: 6374 3.29 - 3.83: 11160 3.83 - 4.36: 12063 4.36 - 4.90: 21978 Nonbonded interactions: 52641 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.224 2.440 nonbonded pdb=" OD1 ASP B 254 " pdb=" N LEU B 255 " model vdw 2.248 2.520 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.270 2.440 nonbonded pdb=" O ILE G 25 " pdb=" NH1 ARG G 27 " model vdw 2.278 2.520 nonbonded pdb=" OG SER R 21 " pdb=" OG SER R 283 " model vdw 2.284 2.440 ... (remaining 52636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.000 Extract box with map and model: 3.650 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 7187 Z= 0.233 Angle : 0.542 8.704 9747 Z= 0.296 Chirality : 0.040 0.137 1113 Planarity : 0.004 0.061 1240 Dihedral : 15.696 90.240 2574 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.13 % Allowed : 18.33 % Favored : 81.54 % 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: 0.93 (0.29), residues: 881 helix: 2.00 (0.28), residues: 370 sheet: 0.51 (0.40), residues: 162 loop : -0.86 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS A 340 PHE 0.010 0.001 PHE R 84 TYR 0.012 0.001 TYR R 299 ARG 0.005 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 206 GLN cc_start: 0.8485 (pt0) cc_final: 0.8273 (pt0) REVERT: B 214 ARG cc_start: 0.8102 (ptp-110) cc_final: 0.7874 (ptp-110) REVERT: R 175 ASN cc_start: 0.8527 (m110) cc_final: 0.8321 (m110) REVERT: R 245 LEU cc_start: 0.8290 (tp) cc_final: 0.8078 (tt) outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 1.2008 time to fit residues: 195.5643 Evaluate side-chains 155 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7187 Z= 0.236 Angle : 0.486 9.476 9747 Z= 0.256 Chirality : 0.041 0.130 1113 Planarity : 0.004 0.049 1240 Dihedral : 4.994 93.443 981 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.92 % Allowed : 17.26 % 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: 0.98 (0.29), residues: 881 helix: 2.12 (0.27), residues: 380 sheet: 0.23 (0.40), residues: 161 loop : -0.84 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR B 145 ARG 0.004 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: B 200 VAL cc_start: 0.8267 (m) cc_final: 0.8002 (p) REVERT: B 214 ARG cc_start: 0.8100 (ptp-110) cc_final: 0.7881 (ptp-110) REVERT: R 245 LEU cc_start: 0.8321 (tp) cc_final: 0.8099 (tt) REVERT: R 274 MET cc_start: 0.6897 (mmt) cc_final: 0.6624 (mmt) outliers start: 22 outliers final: 8 residues processed: 165 average time/residue: 1.2101 time to fit residues: 210.0224 Evaluate side-chains 161 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7187 Z= 0.212 Angle : 0.477 8.918 9747 Z= 0.250 Chirality : 0.041 0.132 1113 Planarity : 0.004 0.049 1240 Dihedral : 4.868 87.343 981 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.45 % Allowed : 18.59 % Favored : 77.95 % 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: 1.08 (0.29), residues: 881 helix: 2.23 (0.27), residues: 383 sheet: 0.27 (0.40), residues: 156 loop : -0.83 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR B 145 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7645 (p0) REVERT: B 200 VAL cc_start: 0.8234 (m) cc_final: 0.7927 (p) REVERT: B 214 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7872 (ptp-110) REVERT: R 245 LEU cc_start: 0.8312 (tp) cc_final: 0.8101 (tt) outliers start: 26 outliers final: 12 residues processed: 173 average time/residue: 1.1504 time to fit residues: 209.8560 Evaluate side-chains 168 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN R 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7187 Z= 0.195 Angle : 0.474 8.892 9747 Z= 0.249 Chirality : 0.040 0.129 1113 Planarity : 0.004 0.047 1240 Dihedral : 4.731 82.584 981 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.72 % Allowed : 18.73 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 881 helix: 2.34 (0.27), residues: 384 sheet: 0.36 (0.41), residues: 149 loop : -0.92 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.011 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7603 (p0) REVERT: B 214 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7871 (ptp-110) REVERT: B 255 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7151 (mp) REVERT: R 245 LEU cc_start: 0.8327 (tp) cc_final: 0.8114 (tt) outliers start: 28 outliers final: 14 residues processed: 171 average time/residue: 1.2098 time to fit residues: 217.8223 Evaluate side-chains 170 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7187 Z= 0.196 Angle : 0.482 9.236 9747 Z= 0.248 Chirality : 0.040 0.132 1113 Planarity : 0.004 0.047 1240 Dihedral : 4.661 78.930 981 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.12 % Allowed : 18.46 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 881 helix: 2.38 (0.28), residues: 384 sheet: 0.38 (0.41), residues: 149 loop : -0.92 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.011 0.001 PHE A 359 TYR 0.009 0.001 TYR A 322 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7601 (p0) REVERT: B 200 VAL cc_start: 0.8286 (m) cc_final: 0.7960 (p) REVERT: B 214 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (ptp-110) REVERT: B 255 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7114 (mp) REVERT: B 262 MET cc_start: 0.7544 (tpp) cc_final: 0.7309 (mpt) REVERT: R 245 LEU cc_start: 0.8328 (tp) cc_final: 0.8112 (tt) outliers start: 31 outliers final: 19 residues processed: 173 average time/residue: 1.1817 time to fit residues: 215.2384 Evaluate side-chains 176 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 285 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN R 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7187 Z= 0.175 Angle : 0.473 8.772 9747 Z= 0.244 Chirality : 0.040 0.131 1113 Planarity : 0.004 0.046 1240 Dihedral : 4.568 76.541 981 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 18.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 881 helix: 2.45 (0.28), residues: 384 sheet: 0.40 (0.41), residues: 149 loop : -0.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.011 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7645 (p0) REVERT: B 200 VAL cc_start: 0.8257 (m) cc_final: 0.7932 (p) REVERT: B 255 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7097 (mp) REVERT: B 298 ASP cc_start: 0.7800 (t0) cc_final: 0.7516 (t70) REVERT: R 245 LEU cc_start: 0.8356 (tp) cc_final: 0.8140 (tt) outliers start: 26 outliers final: 17 residues processed: 166 average time/residue: 1.1660 time to fit residues: 203.9029 Evaluate side-chains 169 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7187 Z= 0.174 Angle : 0.476 8.824 9747 Z= 0.244 Chirality : 0.040 0.131 1113 Planarity : 0.004 0.046 1240 Dihedral : 4.462 73.499 979 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.59 % Allowed : 19.52 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 881 helix: 2.47 (0.28), residues: 384 sheet: 0.27 (0.41), residues: 153 loop : -0.95 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.011 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 363 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7587 (ttm-80) REVERT: B 19 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7507 (ttm-80) REVERT: B 20 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 200 VAL cc_start: 0.8248 (m) cc_final: 0.7929 (p) REVERT: B 255 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7076 (mp) REVERT: B 298 ASP cc_start: 0.7821 (t0) cc_final: 0.7496 (t70) REVERT: R 245 LEU cc_start: 0.8360 (tp) cc_final: 0.8142 (tt) outliers start: 27 outliers final: 17 residues processed: 166 average time/residue: 1.1876 time to fit residues: 207.4282 Evaluate side-chains 169 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7187 Z= 0.180 Angle : 0.483 8.806 9747 Z= 0.248 Chirality : 0.040 0.132 1113 Planarity : 0.004 0.060 1240 Dihedral : 4.406 70.340 979 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.59 % Allowed : 20.19 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 881 helix: 2.45 (0.28), residues: 384 sheet: 0.27 (0.41), residues: 153 loop : -0.96 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.012 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.014 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 363 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7584 (ttm-80) REVERT: B 19 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: B 20 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7613 (p0) REVERT: B 200 VAL cc_start: 0.8242 (m) cc_final: 0.7920 (p) REVERT: B 298 ASP cc_start: 0.7834 (t0) cc_final: 0.7499 (t70) REVERT: R 245 LEU cc_start: 0.8358 (tp) cc_final: 0.8145 (tt) outliers start: 27 outliers final: 16 residues processed: 167 average time/residue: 1.1614 time to fit residues: 204.3569 Evaluate side-chains 168 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN R 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7187 Z= 0.151 Angle : 0.479 8.662 9747 Z= 0.243 Chirality : 0.040 0.134 1113 Planarity : 0.004 0.061 1240 Dihedral : 4.245 66.080 979 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.52 % Allowed : 21.51 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 881 helix: 2.46 (0.28), residues: 386 sheet: 0.35 (0.41), residues: 153 loop : -0.97 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.012 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.015 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7484 (ttm-80) REVERT: B 20 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7607 (p0) REVERT: B 200 VAL cc_start: 0.8253 (m) cc_final: 0.7930 (p) REVERT: B 298 ASP cc_start: 0.7808 (t0) cc_final: 0.7473 (t70) REVERT: B 304 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7697 (ttp80) REVERT: R 13 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7428 (mp) REVERT: R 245 LEU cc_start: 0.8356 (tp) cc_final: 0.8151 (tt) outliers start: 19 outliers final: 12 residues processed: 163 average time/residue: 1.1913 time to fit residues: 205.6124 Evaluate side-chains 167 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 53 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7187 Z= 0.204 Angle : 0.496 8.890 9747 Z= 0.253 Chirality : 0.040 0.131 1113 Planarity : 0.004 0.066 1240 Dihedral : 4.255 62.224 979 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.39 % Allowed : 21.78 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 881 helix: 2.40 (0.28), residues: 385 sheet: 0.40 (0.41), residues: 151 loop : -0.96 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 80 TYR 0.009 0.001 TYR R 104 ARG 0.015 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 363 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7590 (ttm-80) REVERT: B 19 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: B 20 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7605 (p0) REVERT: B 200 VAL cc_start: 0.8249 (m) cc_final: 0.7919 (p) REVERT: B 258 ASP cc_start: 0.7787 (m-30) cc_final: 0.7436 (t70) REVERT: B 298 ASP cc_start: 0.7864 (t0) cc_final: 0.7597 (t0) REVERT: B 304 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7711 (ttp80) REVERT: R 245 LEU cc_start: 0.8359 (tp) cc_final: 0.8143 (tt) outliers start: 18 outliers final: 12 residues processed: 165 average time/residue: 1.2158 time to fit residues: 211.1904 Evaluate side-chains 165 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118080 restraints weight = 10395.168| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.41 r_work: 0.3440 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7187 Z= 0.192 Angle : 0.515 11.328 9747 Z= 0.259 Chirality : 0.040 0.131 1113 Planarity : 0.004 0.066 1240 Dihedral : 4.200 58.592 979 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.26 % Allowed : 21.91 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 881 helix: 2.42 (0.28), residues: 384 sheet: 0.34 (0.41), residues: 152 loop : -1.01 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 80 TYR 0.009 0.001 TYR A 322 ARG 0.015 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.76 seconds wall clock time: 66 minutes 47.41 seconds (4007.41 seconds total)